Method to engineer mammalian-type carbohydrate structures

ABSTRACT

The present invention relates to host cells having modified lipid-linked oligosaccharides which may be modified further by heterologous expression of a set of glycosyltransferases, sugar transporters and mannosidases to become host-strains for the production of mammalian, e.g., human therapeutic glycoproteins. The process provides an engineered host cell which can be used to express and target any desirable gene(s) involved in glycosylation. Host cells with modified lipid-linked oligosaccharides are created or selected. N-glycans made in the engineered host cells have a GlcNAcMan 3 GlcNAc 2  core structure which may then be modified further by heterologous expression of one or more enzymes, e.g., glycosyl-transferases, sugar transporters and mannosidases, to yield human-like glycoproteins. For the production of therapeutic proteins, this method may be adapted to engineer cell lines in which any desired glycosylation structure may be obtained.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. provisional application Ser.No. 60/344,169, Dec. 27, 2001, which is incorporated by reference hereinin its entirety.

FIELD OF THE INVENTION

The present invention generally relates to modifying the glycosylationstructures of recombinant proteins expressed in fungi or other lowereukaryotes, to more closely resemble the glycosylation of proteins ofhigher mammals, in particular humans.

BACKGROUND OF THE INVENTION

After DNA is transcribed and translated into a protein, further posttranslational processing involves the attachment of sugar residues, aprocess known as glycosylation. Different organisms produce differentglycosylation enzymes (glycosyltransferases and glycosidases), and havedifferent substrates (nucleotide sugars) available, so that theglycosylation patterns as well as composition of the individualoligosaccharides, even of one and the same protein, will be differentdepending on the host system in which the particular protein is beingexpressed. Bacteria typically do not glycosylate proteins, and if soonly in a very unspecific manner (Moens, 1997). Lower eukaryotes such asfilamentous fungi and yeast add primarily mannose and mannosylphosphatesugars, whereas insect cells such as Sf9 cells glycosylate proteins inyet another way. See for example (Bretthauer, 1999; Martinet, 1998;Weikert, 1999; Malissard, 2000; Jarvis, 1998; and Takeuchi, 1997).

Synthesis of a mammalian-type oligosaccharide structure consists of aseries of reactions in the course of which sugar-residues are added andremoved while the protein moves along the secretory pathway in the hostorganism. The enzymes which reside along the glycosylation pathway ofthe host organism or cell determine what the resulting glycosylationpatterns of secreted proteins. Unfortunately, the resultingglycosylation pattern of proteins expressed in lower eukaryotic hostcells differs substantially from the glycosylation found in highereukaryotes such as humans and other mammals (Bretthauer, 1999).Moreover, the vastly different glycosylation pattern has, in some cases,been shown to increase the immunogenicity of these proteins in humansand reduce their half-life (Takeuchi, 1997). It would be desirable toproduce human-like glycoproteins in non-human host cells, especiallylower eukaryotic cells.

The early steps of human glycosylation can be divided into at least twodifferent phases: (i) lipid-linked Glc₃Man₉GlcNAc₂ oligosaccharides areassembled by a sequential set of reactions at the membrane of theendoplasmic reticulum (ER) and (ii) the transfer of this oligosaccharidefrom the lipid anchor dolichyl pyrophosphate onto de novo synthesizedprotein. The site of the specific transfer is defined by an asparagine(Asn) residue in the sequence Asn-Xaa-Ser/Thr (see FIG. 1), where Xaacan be any amino acid except proline (Gavel, 1990). Further processingby glucosidases and mannosidases occurs in the ER before the nascentglycoprotein is transferred to the early Golgi apparatus, whereadditional mannose residues are removed by Golgi specific alpha(α)-1,2-mannosidases. Processing continues as the protein proceedsthrough the Golgi. In the medial Golgi, a number of modifying enzymes,including N-acetylglucosaminyltransferases (GnT I, GnT II, GnT III, GnTIV GnT V GnT VI), mannosidase II and fucosyltransferases, add and removespecific sugar residues (see, e.g., FIGS. 2 and 3). Finally, in thetrans-Golgi, galactosyltranferases and sialyltransferases produce aglycoprotein structure that is released from the Golgi. It is thisstructure, characterized by bi-, tri- and tetra-antennary structures,containing galactose, fucose, N-acetylglucosamine and a high degree ofterminal sialic acid, that gives glycoproteins their humancharacteristics.

In nearly all eukaryotes, glycoproteins are derived from the common coreoligosaccharide precursor Glc₃Man₉GlcNAc₂-PP-Dol, where PP-Dol standsfor dolichol-pyrophosphate (FIG. 1). Within the endoplasmic reticulum,synthesis and processing of dolichol pyrophosphate boundoligosaccharides are identical between all known eukaryotes. However,further processing of the core oligosaccharide by yeast, once it hasbeen transferred to a peptide leaving the ER and entering the Golgi,differs significantly from humans as it moves along the secretorypathway and involves the addition of several mannose sugars.

In yeast, these steps are catalyzed by Golgi residingmannosyltransferases, like Och1p, Mnt1p and Mnn1p, which sequentiallyadd mannose sugars to the core oligosaccharide. The resulting structureis undesirable for the production of humanoid proteins and it is thusdesirable to reduce or eliminate mannosyltransferase activity. Mutantsof S. cerevisiae, deficient in mannosyltransferase activity (for exampleoch1 or mnn9 mutants) have been shown to be non-lethal and display areduced mannose content in the oligosacharide of yeast glycoproteins.Other oligosacharide processing enzymes, such as mannosylphophatetransferase may also have to be eliminated depending on the host'sparticular endogenous glycosylation pattern.

Lipid-Linked Oligosaccharide Precursors

Of particular interest for this invention are the early steps ofN-glycosylation (FIGS. 1 and 2). The study of alg (asparagine-linkedglycosylation) mutants defective in the biosynthesis of theGlc₃Man₉GlcNAc₂-PP-Dol has helped to elucidate the initial steps ofN-glycosylation.

The ALG3 gene of S. cerevisiae has been successfully cloned and knockedout by deletion (Aebi, 1996). ALG3 has been shown to encode the enzymeDol-P-Man:Man₅GlcNAc₂-PP-Dol Mannosyltransferase, which is involved inthe first Dol-P-Man dependent mannosylation step from Man₅GlcNAc₂-PP-Dolto Man₆GlcNAc₂-PP-Dol at the luminal side of the ER (Sharma, 2001)(FIGS. 1 and 2). S. cerevisiae cells harboring a leaky alg3-1 mutationaccumulate Man₅GlcNAc₂-PP-Dol (structure I) (Huffaker, 1983).

Man₅GlcNAc₂ (Structure I) and Man₈GlcNAc₂ accumulate in total cellmannoprotein of an och1 mnn1 alg3 mutant(Nakanishi-Shindo, 1993). ThisS. cerevisiae och1, mnn1, alg3 mutant was shown to be viable, buttemperature-sensitive, and to lack α-1,6 polymannose outer chains.

In another study, secretory proteins expressed in a strain deleted foralg 3 (Δalg3 background) were studied for their resistance toEndo-β-N-acetylglucosaminidase H (Endo H) (Aebi, 1996). Previousobservations have indicated that only those oligosaccharides larger thanMan₅GlcNAc₂ are susceptible to cleavage by Endo H (Hubbard, 1980). Inthe alg3-1 phenotype, some glycoforms were sensitive to Endo H cleavage,confirming its leakiness, whereas in the Δalg3 mutant all glycoformsappeared to be resistant and of the Man₅-type (Aebi, 1996), suggesting atight phenotype and transfer of Man₅GlcNAc₂ oligosaccharide structuresonto the nascent polypeptide chain. No obvious phenotype was connectedwith the inactivation of the ALG3 gene (Aebi, 1996). Secretedexogluconase produced in a Saccharomyces cerevisiae alg3 mutant wasfound to contain between 35-44% underglycosylated and unglycosylatedforms and only about 50% of the transferred oligosaccharides remainedresistant to Endo H treatment (Cueva, 1996). Exoglucanase (Exg), anenzyme that contains two potential N-glycosylation sites at Asn₁₆₅ andAsn₃₂₅, was analyzed in more detail. For Exg molecules that received twooligosaccharides it was shown that the first N-glycosylation site(Asn₁₆₅) was enriched in truncated residues, whereas the second (Asn₃₂₅)was enriched in regular oligosaccharides. 35-44% of secretedexoglucanase was non- or underglycosylated and about 73-78% of allavailable N-glycosylation sites were occupied with either truncated orregular oligosaccharides (Cueva, 1996).

Transfer of Glucosylated Lipid-Linked Oligosaccharides

Evidence suggests that, in mammalian cells, only glucosylatedlipid-linked oligosaccharides are transferred to nascent proteins(Turco, 1977), while in yeast alg5, alg6 and dpg1 mutants,nonglucosylated oligosaccharideds can be transferred (Ballou, 1986;Runge, 1984). In a Saccharomyces cerevisiae alg8 mutant,underglucosylated GlcMan₉GlcNAc₂ is transferred (Runge, 1986). Verostekand co-workers studied an alg3, sec18, gls1 mutant and proposed thatglucosylation of a Man₅GlcNAc₂ structure (Structure I, above) isrelatively slow in comparison to glucosylation of a lipid-linked Man₉structure. In addition, the transfer of this Man₅GlcNAc₂ structure toprotein appears to be about 5-fold more efficient than the glucosylationto Glc₃Man₅GlcNAc₂. The decreased rate of Man₅GlcNAc₂ glucosylation incombination with the comparatively faster rate of Man₅ structuretransfer onto nascent protein is believed to be the cause of theobserved accumulation of nonglucosylated Man₅ structures in alg3 mutantyeast (Verostek-a, 1993; Verostek-b, 1993).

Studies preceding the above work did not reveal any lipid-linkedglucosylated oligosaccharides (Orlean, 1990; Huffaker, 1983) allowingthe conclusion that glucosylated oligosaccharides are transferred at amuch higher rate than their nonglucosylated counterparts and thus aremuch harder to isolate. Recent work has allowed the creation and studyof yeast strains with un- and hypoglucosylated oligosaccharides and hasfurther confirmed the importance of the addition of glucose to theantenna of lipid-linked oligosaccharides for substrate recognition bythe oligosaccharyltransferase complex (Reiss, 1996; Stagljar, 1994;Burda, 1998). The decreased degree of glucosylation of the lipid-linkedMan₅-oligosaccharides in an alg3 mutant negatively impacts the kineticsof the transfer of lipid-linked oligosaccharides onto nascent proteinand is believed to be the cause for the strong underglycosylation ofsecreted proteins in an alg3 knock-out strain (Aebi, 1996).

The assembly of the lipid-linked core oligosaccharide Man₉GlcNAc₂occurs, as described above, at the membrane of the endoplasmaticreticulum. The additions of three glucose units to the α-1,3-antenna ofthe lipid-linked oligosaccharides are the final reactions in theoligosaccharide assembly. First an α-1,3 glucose residue is addedfollowed by another α-1,3 glucose residue and a terminal α-1,2 glucoseresidue. Mutants accumulating dolichol-linked Man₉GlcNAc₂ have beenshown to be defective in the ALG6 locus, and Alg6p has similarities toAlg8p, the α-1,3-glucosyltransferase catalyzing the addition of thesecond α-1,3-linked glucose (Reiss, 1996). Cells with a defective ALG8locus accumulate dolichol-linked Glc₁Man₉GlcNAc₂ (Runge, 1986; Stagljar,1994). The ALG10 locus encodes the α-1,2 glucosyltransferase responsiblefor the addition of a single terminal glucose to Glc₂Man₉GlcNAc₂-PP-Dol(Burda, 1998).

Sequential Processing of N-Glycans by Localized Enzyme Activities

Sugar transferases and mannosidases line the inner (luminal) surface ofthe ER and Golgi apparatus and thereby provide a “catalytic” surfacethat allows for the sequential processing of glycoproteins as theyproceed through the ER and Golgi network. In fact the multiplecompartments of the cis, medial, and trans Golgi and the trans-GolgiNetwork (TGN), provide the different localities in which the orderedsequence of glycosylation reactions can take place. As a glycoproteinproceeds from synthesis in the ER to full maturation in the late Golgior TGN, it is sequentially exposed to different glycosidases,mannosidases and glycosyltransferases such that a specific carbohydratestructure may synthesized. Much work has been dedicated to revealing theexact mechanism by which these enzymes are retained and anchored totheir respective organelle. The evolving picture is complex but evidencesuggests that, stem region, membrane spanning region and cytoplasmictail individually or in concert direct enzymes to the membrane ofindividual organelles and thereby localize the associated catalyticdomain to that locus.

In some cases these specific interactions were found to function acrossspecies. For example the membrane spanning domain of α2,6-ST from rats,an enzyme known to localize in the trans-Golgi of the animal, was shownto also localize a reporter gene (invertase) in the yeast Golgi(Schwientek, 1995). However, the very same membrane spanning domain aspart of a full-length α2,6 ST was retained in the ER and not furthertransported to the Golgi of yeast (Krezdorn, 1994). A full length Gal-Trfrom humans was not even synthesized in yeast, despite demonstrably hightranscription levels. On the other hand the transmembrane region ofhuman the same GalT fused to an invertase reporter was able to directlocalization to the yeast Golgi, albeit it at low production levels.Schwientek and co-workers have shown that fusing 28 amino acids of ayeast mannosyltransferase (Mnt1), a region containing a cytoplamic tail,a transmembrane region and eight amino acids of the stem region, to thecatalytic domain of human GalT are sufficient for Golgi localization ofan active GalT. Other galactosyltransferases appear to rely oninteractions with enzymes resident in particular organelles since afterremoval of their transmembrane region they are still able to localizeproperly. To date there exists no reliable way of predicting whether aparticular heterologously expressed glycosyltransferase or mannosidasein a lower eukaryote will be (1), sufficiently translated (2),catalytically active or (3) located to the proper organelle within thesecretory pathway. Since all three of these are necessary to effectglycosylation patterns in lower eukaryotes, a systematic scheme toachieve the desired catalytic function and proper retention of enzymesin the absence of predictive tools, which are currently not available,has been designed.

Production of Therapeutic Glycoproteins

A significant number of proteins isolated from humans or animals arepost-translationally modified, with glycosylation being one of the mostsignificant modifications. An estimated 70% of all therapeutic proteinsare glycosylated and thus currently rely on a production system (i.e.,host cell) that is able to glycosylate in a manner similar to humans. Todate, most glycoproteins are made in a mammalian host system. Severalstudies have shown that glycosylation plays an important role indetermining the (1) immunogenicity, (2) pharmacokinetic properties, (3)trafficking, and (4) efficacy of therapeutic proteins. It is thus notsurprising that substantial efforts by the pharmaceutical industry havebeen directed at developing processes to obtain glycoproteins that areas “humanoid” or “human-like” as possible. This may involve the geneticengineering of such mammalian cells to enhance the degree of sialylation(i.e., terminal addition of sialic acid) of proteins expressed by thecells, which is known to improve pharmacokinetic properties of suchproteins. Alternatively one may improve the degree of sialylation by invitro addition of such sugars using known glycosyltransferases and theirrespective nucleotide sugars (e.g., 2,3 sialyltransferase and CMP-Sialicacid).

Future research may reveal the biological and therapeutic significanceof specific glycoforms, thereby rendering the ability to produce suchspecific glycoforms desirable. To date, efforts have concentrated onmaking proteins with fairly well characterized glycosylation patterns,and expressing a cDNA encoding such a protein in one of the followinghigher eukaryotic protein expression systems:

-   -   1. Higher eukaryotes such as Chinese hamster ovary cells (CHO),        mouse fibroblast cells and mouse myeloma cells (Werner, 1998);    -   2. Transgenic animals such as goats, sheep, mice and others        (Dente, 1988); (Cole, 1994); (McGarvey, 1995); (Bardor, 1999);    -   3. Plants (Arabidopsis thaliana, tobacco etc.) (Staub, 2000);        (McGarvey, 1995); (Bardor, 1999);    -   4. Insect cells (Spodoptera frugiperda Sf9, Sf21, Trichoplusia        ni, etc., in combination with recombinant baculoviruses such as        Autographa californica multiple nuclear polyhedrosis virus which        infects lepidopteran cells (Altmann, 1999).

While most higher eukaryotes carry out glycosylation reactions that aresimilar to those found in humans, recombinant human proteins expressedin the above mentioned host systems invariably differ from their“natural” human counterpart (Raju, 2000). Extensive development work hasthus been directed at finding ways to improving the “human character” ofproteins made in these expression systems. This includes theoptimization of fermentation conditions and the genetic modification ofprotein expression hosts by introducing genes encoding enzymes involvedin the formation of human like glycoforms (Werner, 1998); (Weikert,1999); (Andersen, 1994); (Yang, 2000). Inherent problems associated withall mammalian expression systems have not been solved.

Fermentation processes based on mammalian cell culture (e.g., CHO,murine, or human cells), for example, tend to be very slow (fermentationtimes in excess of one week are not uncommon), often yield low producttiters, require expensive nutrients and cofactors (e.g., bovine fetalserum), are limited by programmed cell death (apoptosis), and often donot enable expression of particular therapeutically valuable proteins.More importantly, mammalian cells are susceptible to viruses that havethe potential to be human pathogens and stringent quality controls arerequired to assure product safety. This is of particular concern sincemany such processes require the addition of complex and temperaturesensitive media components that are derived from animals (e.g., bovinecalf serum), which may carry agents pathogenic to humans such as bovinespongiform encephalopathy (BSE) prions or viruses. Moreover, theproduction of therapeutic compounds is preferably carried out in awell-controlled sterile environment. An animal farm, no matter howcleanly kept, does not constitute such an environment, thus constitutingan additional problem in the use of transgenic animals for manufacturinghigh volume therapeutic proteins.

Most, if not all, currently produced therapeutic glycoproteins aretherefore expressed in mammalian cells and much effort has been directedat improving (i.e., “humanizing”) the glycosylation pattern of theserecombinant proteins. Changes in medium composition as well as theco-expression of genes encoding enzymes involved in human glycosylationhave been successfully employed (see, for example, Weikert, 1999).

While recombinant proteins similar to their human counterparts can bemade in mammalian expression systems, it is currently not possible tomake proteins with a human-like glycosylation pattern in lowereukaryotes (fungi and yeast). Although the core oligosaccharidestructure transferred to a protein in the endoplasmic reticulum isbasically identical in mammals and lower eukaryotes, substantialdifferences have been found in the subsequent processing reactions whichoccur in in the Golgi apparatus of fungi and mammals. In fact, evenamongst different lower eukaryotes there exist a great variety ofglycosylation structures. This has prevented the use of lower eukaryotesas hosts for the production of recombinant human glycoproteins despiteotherwise notable advantages over mammalian expression systems, such as:(1) generally higher product titers, (2) shorter fermentation times, (3)having an alternative for proteins that are poorly expressed inmammalian cells, (4) the ability to grow in a chemically defined proteinfree medium and thus not requiring complex animal derived mediacomponents, (5) and the absence of viral, especially retroviralinfections of such hosts.

Various methylotrophic yeasts such as Pichia pastoris, Pichiamethanolica, and Hansenula polymorpha, have played particularlyimportant roles as eukaryotic expression systems because they are ableto grow to high cell densities and secrete large quantities ofrecombinant protein. However, as noted above, lower eukaryotes such asyeast do not glycosylate proteins like higher mammals. See for example,Martinet et al. (1998) Biotechnol Let. Vol. 20. No. 12, which disclosesthe expression of a heterologous mannosidase in the endoplasmicreticulum (ER).

Chiba et al. (1998) have shown that S. cerevisiae can be engineered toprovide structures ranging from Man₈GlcNAc₂ to Man₅GlcNAc₂ structures,by eliminating 1,6 mannosyltransferase (OCH1), 1,3 mannosyltransferase(MNN1) and a regulator of mannosylphosphatetransferase (MNN4) and bytargeting the catalytic domain of α-1,2-mannosidase I from Aspergillussaitoi into the ER of S. cerevisiae using an ER retrieval sequence(Chiba, 1998). However, this attempt resulted in little or no productionof the desired Man₅GlcNAc₂, e.g., one that was made in vivo and whichcould function as a substrate for GnT1 (the next step in makinghuman-like glycan structures). Chiba et al. (1998) showed that P.pastoris is not inherently able to produce useful quantities (greaterthan 5%) of GlcNAcTransferase I accepting carbohydrate.

Maras and co-workers assert that in T. reesei “sufficient concentrationsof acceptor substrate (i.e. Man₅GlcNAc₂) are present”, however whentrying to convert this acceptor substrate to GlcNAcMan₅GlcNAc₂ in vitroless than 2% were converted thereby demonstrating the presence ofMan₅GlcNAc₂ structures that are not suitable precursors for complexN-glycan formation (Maras, 1997; Maras, 1999). To date no enablingdisclosure exists, that allows for the production of commerciallyrelevant quantities of GlcNAcMan₅GlcNAc₂ in lower eukaryotes.

It is therefore an object of the present invention to provide a systemand methods for humanizing glycosylation of recombinant glycoproteinsexpressed in non-human host cells.

SUMMARY OF THE INVENTION

The present invention relates to host cells such as fungal strainshaving modified lipid-linked oligosaccharides which may be modifiedfurther by heterologous expression of a set of glycosyltransferases,sugar transporters and mannosidases to become host-strains for theproduction of mammalian, e.g., human therapeutic glycoproteins. Aprotein production method has been developed using (1) a lowereukaryotic host such as a unicellular or filamentous fungus, or (2) anynon-human eukaryotic organism that has a different glycosylation patternfrom humans, to modify the glycosylation composition and structures ofthe proteins made in a host organism (“host cell”) so that they resemblemore closely carbohydrate structures found in human proteins. Theprocess allows one to obtain an engineered host cell which can be usedto express and target any desirable gene(s) involved in glycosylation bymethods that are well established in the scientific literature andgenerally known to the artisan in the field of protein expression. Asdescribed herein, host cells with modified lipid-linked oligosaccharidesare created or selected. N-glycans made in the engineered host cellshave a GlcNAcMan₃GlcNAc₂ core structure which may then be modifiedfurther by heterologous expression of one or more enzymes, e.g.,glycosyl-transferases, sugar transporters and mannosidases, to yieldhuman-like glycoproteins. For the production of therapeutic proteins,this method may be adapted to engineer cell lines in which any desiredglycosylation structure may be obtained.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic of the structure of the dolichylpyrophosphate-linked oligosaccharide.

FIGS. 2A-2Bshow a schematic of the generation of GlcNAc₂Man₃GlcNAc₂N-glycans from fungal host cells which are deficient in alg3, alg9 oralg 12 activities.

FIG. 3 is a schematic of processing reactions required to producemammalian-type oligosaccharide structures in a fungal host cell with analg3, och1 genotype.

FIGS. 4A-4F

-   -   SEQ ID NO:24 S. Cerevisiae (Query 1)    -   SEQ ID NO:25 S. Cerevisiae (Subject 1)    -   SEQ ID NO:26 S. Cerevisiae (Query)    -   SEQ ID NO:27 H. sapiens (Subject)    -   SEQ ID NO:28 S. Cerevisiae (Query 1)    -   SEQ ID NO:29 Drosophilia virilis (Subject)    -   SEQ ID NO:30 S. Cerevisiae (Query)    -   SEQ ID NO:31 Drosophila melanogaster (Subject)

FIG. 5

-   -   SEQ ID NO:32 DNA sequence    -   SEQ ID NO:33 amino acid sequence

FIG. 6

-   -   SEQ ID NO:34 DNA sequence    -   SEQ ID NO:35 amino acid sequence

FIGS. 7A-7D

-   -   SEQ ID NO:36 Pichia Pastoris (Query)    -   SEQ ID NO:37 S. Cerevisiae (Subject)    -   SEQ ID NO:38 (Query)    -   SEQ ID NO:39 Neurospora Crassa (Subject)    -   SEQ ID NO:40 Pichia Patoris (Query)    -   SEQ ID NO:41 Schizosaccharomyces pombe (Subject)    -   SEQ ID NO:42 Pichia Pastoris    -   SEQ ID NO:43 Arabidopsis thaliana

FIG. 8

-   -   SEQ ID NO:44 DNA sequence    -   SEQ ID NO:45 amino acid sequence

FIG. 9

-   -   SEQ ID NO:46 K. lactis    -   SEQ ID NO:47 S. Cerevisiae    -   SEQ ID NO:48 K. lactis    -   SEQ ID NO:49 Arabidopsis thaliana

FIG. 10

-   -   SEQ ID NO:50 S. Cerevisiae Alg 9 DNA    -   SEQ ID NO:51 S. Cerevisiae amino acid

FIG. 11

-   -   SEQ ID NO:52 Pichia Pastoris Alg 9 DNA    -   SEQ ID NO:53 Pichia Pastoris amino acid

FIGS. 12A-12C

-   -   SEQ ID NO:54 Pichia Pastoris (Query)    -   SEQ ID NO:55 S. Cerevisiae (Subject)    -   SEQ ID NO:56 Pichia Pastoris (Query)    -   SEQ ID NO:57 Anopheles gambiae (Subject)    -   SEQ ID NO:58 Pichia Pastoris (Query)    -   SEQ ID NO:59 S. pombe (Subject)    -   SEQ ID NO:60 Pichia Pastoris (Query)    -   SEQ ID NO:61 M. Musculus (Subject)    -   SEQ ID NO:62 Pichia Pastoris (Query)    -   SEQ ID NO:63 H. Sapiens (Subject)

FIG. 13

-   -   SEQ ID NO:64 S. Cerevisiae Alg 12 DNA    -   SEQ ID NO:65 S. Cerevisiae Alg 12 amino acid

FIG. 14

-   -   SEQ ID NO:66 Pichia Pastoris Alg 12 DNA    -   SEQ ID NO:67 S. Cerevisiae Alg 12 amino acid

FIGS. 15A-15B

-   -   SEQ ID NO:68 Pichia Pastoris (Query)    -   SEQ ID NO:69 S. Cerevisiae (Subject)    -   SEQ ID NO:70 Pichia Pastoris (Query)    -   SEQ ID NO:71 S. pombe (Subject)    -   SEQ ID NO:72 Pichia Pastoris (Query)    -   SEQ ID NO:73 S. pombe (Subject)

FIG. 16 is a MALDI-TOF-MS analysis of N-glycans isolated from a kringle3 glycoprotein produced in a P. pastoris showing that the predominantN-glycan is GlcNAcMan₅GlcNAc₂.

FIG. 17 is a MALDI-TOF-MS analysis of N-glycans isolated from a kringle3 glycoprotein produced in a P. pastoris (FIG. 16) treated withβ-N-hexosaminidase (peak corresponding to Man₅GlcNAc₂) to confirm thatthe predominant N-glycan of FIG. 16 is GlcNAcMan₅GlcNAc₂.

FIG. 18 is a MALDI-TOF-MS analysis of N-glycans isolated from a kringle3 glycoprotein produced in a P. pastoris alg3 deletion mutant showingthat the predominant N-glycans are GlcNAcMan₃GlcNAc₂ andGlcNAcMan₄GlcNAc₂.

FIG. 19 is a MALDI-TOF-MS analysis of N-glycans isolated from a kringle3 glycoprotein produced in a P. pastoris alg3 deletion mutant treatedwith α1,2 marmosidase, showing that the GlcNAcMan₄GlcNAc₂ of FIG. 18 isconverted to GlcNAcMan₃GlcNAc₂.

FIG. 20 is a MALDI-TOF-MS analysis of N-glycans of FIG. 19 treated withβ-N-hexosaminidase (peak corresponding to Man₃GlcNAc₂) to confirm thatthe N-glycan of FIG. 19 is GlcNAcMan₃GlcNAc₂.

FIG. 21 is a MALDI-TOF-MS analysis of N-glycans isolated from a kringle3 glycoprotein produced in a P. pastoris alg3 deletion mutant treatedwith α1,2 mannosidase and GnTII, showing that the GlcNAcMan₃GlcNAc₂ ofFIG. 19 is converted to GlcNAc₂Man₃GlcNAc₂.

FIG. 22 is a MALDI-TOF-MS analysis of N-glycans of FIG. 21 treated withβ-N-hexosaminidase (peak corresponding to Man₃GlcNAc₂) to confirm thatthe N-glycan of FIG. 21 is GlcNAc₂Man₃GlcNAc₂.

FIG. 23 is a MALDI-TOF-MS analysis of N-glycans isolated from a kringle3 glycoprotein produced in a P. pastoris alg3 deletion mutant treatedwith α1,2 mannosidase and GnTII in the presence of UDP-galactose andβ1,4-galactosyltransferase, showing that the GlcNAc₂Man₃GlcNAc₂ of FIG.21 is converted to Gal₂GlcNAc₂Man₃GlcNAc₂.

FIG. 24 is a MALDI-TOF-MS analysis of N-glycans isolated from a kringle3 glycoprotein produced in a P. pastoris alg3 deletion mutant treatedwith α1,2 mannosidase and GnTII in the presence of UDP-galactose andβ1,4-galactosyltransferase, and further treated withCMP-N-acetylneuraminic acid and sialyltransferase, showing that theGal₂GlcNAc₂Man₃GlcNAc₂ is converted to NANA₂Gal₂GlcNAc₂Man₃GlcNAc₂,

FIGS. 25A-25B

-   -   SEQ ID NO:74 S. Cerevisiae DNA Alg 6    -   SEQ ID NO:75 S. Cerevisiae amino acid    -   SEQ ID NO:76 Pichia Pastoris DNA Alg 6    -   SEQ ID NO:77 Pichia Pastoris amino acid Alg 6

FIGS. 26A-26B

-   -   SEQ ID NO:78 Pichia Pastoris (Query)    -   SEQ ID NO:79 S. Cerevisiae (Subject)    -   SEQ ID NO:80 Pichia Pastoris (Query)    -   SEQ ID NO:81 S. pombe (Subject)    -   SEQ ID NO:82 Pichia Pastoris (Query)    -   SEQ ID NO:83 D. melanogaster (Subject)    -   SEQ ID NO:84 Pichia Pastoris (Query)    -   SEQ ID NO:85 A. thaliana (Subject)

FIGS. 27A-27E show P. pastoris Alg 6 Sequence Comparisons (Blast)

FIG. 28

-   -   SEQ ID NO:86 K. lactis Alg 6 DNA    -   SEQ ID NO:87 K. lactis Alg 6 amino acid

FIGS. 29A-29C

-   -   SEQ ID NO:88 K. lactis Alg 6 DNA    -   SEQ ID NO:89 S. Cerevisiae (Subject)    -   SEQ ID NO:90 K. lactis (Query)    -   SEQ ID NO:91 S. pombe (Subject)    -   SEQ ID NO:92 K. lactis (Query)    -   SEQ ID NO:93 A. thaliana (Subject)    -   SEQ ID NO:94 K. lactis (Query)    -   SEQ ID NO:95 H. Sapiens (Subject)

FIG. 30 Model of an IgG immunoglobulin. Heavy chain and light chain canbe, based on similar secondary and tertiary structure, subdivided intodomains. The two heavy chains (domains V_(H), C_(H)1, C_(H)2 and C_(H)3)are linked through three disulfide bridges. The light chains (domainsV_(L) and C_(L)) are linked by another disulfide bridge to the C_(H)1portion of the heavy chain and, together with the C_(H)1 and V_(H)fragments, make up the Fab region. Antigens bind to the terminal portionof the Fab region. Effector-functions, such as Fc-gamma-Receptor bindinghave been localized to the C_(H)2 domain, just downstream of the hingeregion and are influenced by N-glycosylation of asparagine 297 in theheavy chain.

FIG. 31 Schematic overview of a modular IgG1 expression vector.

FIG. 32

-   -   SEQ ID NO:96 M. musculus DNA GnTIII    -   SEQ ID NO:97 M. musculus amino acid GnTIII

FIGS. 33A-33B

-   -   SEQ ID NO:98 H. Sapiens DNA GnTIV    -   SEQ ID NO:99 H. Sapiens aa Gn TIV

FIGS. 34A-34B

-   -   SEQ ID NO:100 M. musculus DNA GnTV    -   SEQ ID NO:101 M. musculus aa GnTV

DETAILED DESCRIPTION OF THE INVENTION

Unless otherwise defined herein, scientific and technical terms used inconnection with the present invention shall have the meanings that arecommonly understood by those of ordinary skill in the art. Further,unless otherwise required by context, singular terms shall includepluralities and plural terms shall include the singular. The methods andtechniques of the present invention are generally performed according toconventional methods well known in the art. Generally, nomenclaturesused in connection with, and techniques of biochemistry, enzymology,molecular and cellular biology, microbiology, genetics and protein andnucleic acid chemistry and hybridization described herein are those wellknown and commonly used in the art. The methods and techniques of thepresent invention are generally performed according to conventionalmethods well known in the art and as described in various general andmore specific references that are cited and discussed throughout thepresent specification unless otherwise indicated. See, e.g., Sambrook etal. Molecular Cloning: A Laboratory Manual, 2d ed., Cold Spring HarborLaboratory Press, Cold Spring Harbor, N.Y. (1989); Ausubel et al.,Current Protocols in Molecular Biology, Greene Publishing Associates(1992, and Supplements to 2002); Harlow and Lane Antibodies: ALaboratory Manual Cold Spring Harbor Laboratory Press, Cold SpringHarbor, N.Y. (1990); Introduction to Glycobiology, Maureen E. Taylor,Kurt Drickamer, Oxford Univ. Press (2003); Worthington Enzyme Manual,Worthington Biochemical Corp. Freehold, N.J.; Handbook of Biochemistry:Section A Proteins Vol I 1976 CRC Press; Handbook of Biochemistry:Section A Proteins Vol II 1976 CRC Press; Essentials of Glycobiology,Cold Spring Harbor Laboratory Press (1999). The nomenclatures used inconnection with, and the laboratory procedures and techniques of,biochemistry and molecular biology described herein are those well knownand commonly used in the art.

All publications, patents and other references mentioned herein areincorporated by reference.

The following terms, unless otherwise indicated, shall be understood tohave the following meanings:

As used herein, the term “N-glycan” refers to an N-linkedoligosaccharide, e.g., one that is attached by anasparagine-N-acetylglucosamine linkage to an asparagine residue of apolypeptide. N-glycans have a common pentasaccharide core of Man₃GlcNAc₂(“Man” refers to mannose; “Glc” refers to glucose; and “NAc” refers toN-acetyl; GlcNAc refers to N-acetylglucosamine). N-glycans differ withrespect to the number of branches (antennae) comprising peripheralsugars (e.g., fucose and sialic acid) that are added to the Man₃GlcNAc₂(“Man3”) core structure. N-glycans are classified according to theirbranched constituents (e.g., high mannose, complex or hybrid). A “highmannose” type N-glycan has five or more mannose residues. A “complex”type N-glycan typically has at least one GlcNAc attached to the 1,3mannose arm and at least one GlcNAc attached to the 1,6 mannose arm of a“trimannose” core. The “trimannose core” is the pentasaccharide corehaving a Man3 structure. Complex N-glycans may also have galactose(“Gal”) residues that are optionally modified with sialic acid orderivatives (“NeuAc”, where “Neu” refers to neuraminic acid and “Ac”refers to acetyl). Complex N-glycans may also have intrachainsubstitutions comprising “bisecting” GlcNAc and core fucose (“Fuc”). A“hybrid” N-glycan has at least one GlcNAc on the terminal of the 1,3mannose arm of the trimannose core and zero or more mannoses on the 1,6mannose arm of the trimannose core.

Abbreviations used herein are of common usage in the art, see, e.g.,abbreviations of sugars, above. Other common abbreviations include“PNGase”, which refers to peptide N-glycosidase F (EC 3.2.2.18); “GlcNAcTr (I-III)”, which refers to one of threeN-acetylglucosaminyltransferase enzymes; “NANA” refers toN-acetylneuraminic acid.

As used herein, the term “secretion pathway” refers to the assembly lineof various glycosylation enzymes to which a lipid-linked oligosaccharideprecursor and an N-glycan substrate are sequentially exposed, followingthe molecular flow of a nascent polypeptide chain from the cytoplasm tothe endoplasmic reticulum (ER) and the compartments of the Golgiapparatus. Enzymes are said to be localized along this pathway. Anenzyme X that acts on a lipid-linked glycan or an N-glycan before enzymeY is said to be or to act “upstream” to enzyme Y; similarly, enzyme Y isor acts “downstream” from enzyme X.

As used herein, the term “alg X activity” refers to the enzymaticactivity encoded by the “alg X” gene, and to an enzyme having thatenzymatic activity encoded by a homologous gene or gene product (seebelow) or by an unrelated gene or gene product.

As used herein, the term “antibody” refers to a full antibody(consisting of two heavy chains and two light chains) or a fragmentthereof. Such fragments include, but are not limited to, those producedby digestion with various proteases, those produced by chemical cleavageand/or chemical dissociation, and those produced recombinantly, so longas the fragment remains capable of specific binding to an antigen. Amongthese fragments are Fab, Fab′, F(ab′)2, and single chain Fv (scFv)fragments. Within the scope of the term “antibody” are also antibodiesthat have been modified in sequence, but remain capable of specificbinding to an antigen. Example of modified antibodies are interspecieschimeric and humanized antibodies; antibody fusions; and heteromericantibody complexes, such as diabodies (bispecific antibodies),single-chain diabodies, and intrabodies (see, e.g., Marasco (ed.),Intracellular Antibodies: Research and Disease Applications,Springer-Verlag New York, Inc. (1998) (ISBN: 3540641513), the disclosureof which is incorporated herein by reference in its entirety).

As used herein, the term “mutation” refers to any change in the nucleicacid or amino acid sequence of a gene product, e.g., of aglycosylation-related enzyme.

The term “polynucleotide” or “nucleic acid molecule” refers to apolymeric form of nucleotides of at least 10 bases in length. The termincludes DNA molecules (e.g., cDNA or genomic or synthetic DNA) and RNAmolecules (e.g., mRNA or synthetic RNA), as well as analogs of DNA orRNA containing non-natural nucleotide analogs, non-nativeinternucleoside bonds, or both. The nucleic acid can be in anytopological conformation. For instance, the nucleic acid can besingle-stranded, double-stranded, triple-stranded, quadruplexed,partially double-stranded, branched, hairpinned, circular, or in apadlocked conformation. The term includes single and double strandedforms of DNA.

Unless otherwise indicated, a “nucleic acid comprising SEQ ID NO:X”refers to a nucleic acid, at least a portion of which has either (i) thesequence of SEQ ID NO:X, or (ii) a sequence complementary to SEQ IDNO:X. The choice between the two is dictated by the context. Forinstance, if the nucleic acid is used as a probe, the choice between thetwo is dictated by the requirement that the probe be complementary tothe desired target.

An “isolated” or “substantially pure” nucleic acid or polynucleotide(e.g., an RNA, DNA or a mixed polymer) is one which is substantiallyseparated from other cellular components that naturally accompany thenative polynucleotide in its natural host cell, e.g., ribosoines,polymerases, and genomic sequences with which it is naturallyassociated. The term embraces a nucleic acid or polynucleotide that (1)has been removed from its naturally occurring environment, (2) is notassociated with all or a portion of a polynucleotide in which the“isolated polynucleotide” is found in nature, (3) is operatively linkedto a polynucleotide which it is not linked to in nature, or (4) does notoccur in nature. The term “isolated” or “substantially pure” also can beused in reference to recombinant or cloned DNA isolates, chemicallysynthesized polynucleotide analogs, or polynucleotide analogs that arebiologically synthesized by heterologous systems.

However, “isolated” does not necessarily require that the nucleic acidor polynucleotide so described has itself been physically removed fromits native environment. For instance, an endogenous nucleic acidsequence in the genome of an organism is deemed “isolated” herein if aheterologous sequence (i.e., a sequence that is not naturally adjacentto this endogenous nucleic acid sequence) is placed adjacent to theendogenous nucleic acid sequence, such that the expression of thisendogenous nucleic acid sequence is altered. By way of example, anon-native promoter sequence can be substituted (e.g., by homologousrecombination) for the native promoter of a gene in the genome of ahuman cell, such that this gene has an altered expression pattern. Thisgene would now become “isolated” because it is separated from at leastsome of the sequences that naturally flank it.

A nucleic acid is also considered “isolated” if it contains anymodifications that do not naturally occur to the corresponding nucleicacid in a genome. For instance, an endogenous coding sequence isconsidered “isolated” if it contains an insertion, deletion or a pointmutation introduced artificially, e.g., by human intervention. An“isolated nucleic acid” also includes a nucleic acid integrated into ahost cell chromosome at a heterologous site, a nucleic acid constructpresent as an episome. Moreover, an “isolated nucleic acid” can besubstantially free of other cellular material, or substantially free ofculture medium when produced by recombinant techniques, or substantiallyfree of chemical precursors or other chemicals when chemicallysynthesized.

As used herein, the phrase “degenerate variant” of a reference nucleicacid sequence encompasses nucleic acid sequences that can be translated,according to the standard genetic code, to provide an amino acidsequence identical to that translated from the reference nucleic acidsequence.

The term “percent sequence identity” or “identical” in the context ofnucleic acid sequences refers to the residues in the two sequences whichare the same when aligned for maximum correspondence. The length ofsequence identity comparison may be over a stretch of at least aboutnine nucleotides, usually at least about 20 nucleotides, more usually atleast about 24 nucleotides, typically at least about 28 nucleotides,more typically at least about 32 nucleotides, and preferably at leastabout 36 or more nucleotides. There are a number of different algorithmsknown in the art which can be used to measure nucleotide sequenceidentity. For instance, polynucleotide sequences can be compared usingFASTA, Gap or Bestfit, which are programs in Wisconsin Package Version10.0, Genetics Computer Group (GCG), Madison, Wis. FASTA providesalignments and percent sequence identity of the regions of the bestoverlap between the query and search sequences (Pearson, 1990, (hereinincorporated by reference). For instance, percent sequence identitybetween nucleic acid sequences can be determined using FASTA with itsdefault parameters (a word size of 6 and the NOPAM factor for thescoring matrix) or using Gap with its default parameters as provided inGCG Version 6.1, herein incorporated by reference.

The term “substantial homology” or “substantial similarity,” whenreferring to a nucleic acid or fragment thereof, indicates that, whenoptimally aligned with appropriate nucleotide insertions or deletionswith another nucleic acid (or its complementary strand), there isnucleotide sequence identity in at least about 50%, more preferably 60%of the nucleotide bases, usually at least about 70%, more usually atleast about 80%, preferably at least about 90%, and more preferably atleast about 95%, 96%, 97%, 98% or 99% of the nucleotide bases, asmeasured by any well-known algorithm of sequence identity, such asFASTA, BLAST or Gap, as discussed above.

Alternatively, substantial homology or similarity exists when a nucleicacid or fragment thereof hybridizes to another nucleic acid, to a strandof another nucleic acid, or to the complementary strand thereof, understringent hybridization conditions. “Stringent hybridization conditions”and “stringent wash conditions” in the context of nucleic acidhybridization experiments depend upon a number of different physicalparameters. Nucleic acid hybridization will be affected by suchconditions as salt concentration, temperature, solvents, the basecomposition of the hybridizing species, length of the complementaryregions, and the number of nucleotide base mismatches between thehybridizing nucleic acids, as will be readily appreciated by thoseskilled in the art. One having ordinary skill in the art knows how tovary these parameters to achieve a particular stringency ofhybridization.

In general, “stringent hybridization” is performed at about 25° C. belowthe thermal melting point (T_(m)) for the specific DNA hybrid under aparticular set of conditions. “Stringent washing” is performed attemperatures about 5° C. lower than the T_(m) for the specific DNAhybrid under a particular set of conditions. The T_(m) is thetemperature at which 50% of the target sequence hybridizes to aperfectly matched probe. See Sambrook et al., supra, page 9.51, herebyincorporated by reference. For purposes herein, “high stringencyconditions” are defined for solution phase hybridization as aqueoushybridization (i.e., free of formamide) in 6×SSC (where 20×SSC contains3.0 M NaCl and 0.3 M sodium citrate), 1% SDS at 65° C. for 8-12 hours,followed by two washes in 0.2×SSC, 0.1% SDS at 65° C. for 20 minutes. Itwill be appreciated by the skilled worker that hybridization at 65° C.will occur at different rates depending on a number of factors includingthe length and percent identity of the sequences which are hybridizing.

The nucleic acids (also referred to as polynucleotides) of thisinvention may include both sense and antisense strands of RNA, cDNA,genomic DNA, and synthetic forms and mixed polymers of the above. Theymay be modified chemically or biochemically or may contain non-naturalor derivatized nucleotide bases, as will be readily appreciated by thoseof skill in the art. Such modifications include, for example, labels,methylation, substitution of one or more of the naturally occurringnucleotides with an analog, internucleotide modifications such asuncharged linkages (e.g., methyl phosphonates, phosphotriesters,phosphoramidates, carbamates, etc.), charged linkages (e.g.,phosphorothioates, phosphorodithioates, etc.), pendent moieties (e.g.,polypeptides), intercalators (e.g., acridine, psoralen, etc.),chelators, alkylators, and modified linkages (e.g., alpha anomericnucleic acids, etc.) Also included are synthetic molecules that mimicpolynucleotides in their ability to bind to a designated sequence viahydrogen bonding and other chemical interactions. Such molecules areknown in the art and include, for example, those in which peptidelinkages substitute for phosphate linkages in the backbone of themolecule.

The term “mutated” when applied to nucleic acid sequences means thatnucleotides in a nucleic acid sequence may be inserted, deleted orchanged compared to a reference nucleic acid sequence. A singlealteration may be made at a locus (a point mutation) or multiplenucleotides may be inserted, deleted or changed at a single locus. Inaddition, one or more alterations may be made at any number of lociwithin a nucleic acid sequence. A nucleic acid sequence may be mutatedby any method known in the art including but not limited to mutagenesistechniques such as “error-prone PCR” (a process for performing PCR underconditions where the copying fidelity of the DNA polymerase is low, suchthat a high rate of point mutations is obtained along the entire lengthof the PCR product. See, e.g., Leung, D. W., et al., Technique, 1, pp.11-15 (1989) and Caldwell, R. C. & Joyce G. F., PCR Methods Applic., 2,pp. 28-33 (1992)); and “oligonucleotide-directed mutagenesis” (a processwhich enables the generation of site-specific mutations in any clonedDNA segment of interest. See, e.g., Reidhaar-Olson, J. F. & Sauer, R.T., et al., Science, 241, pp. 53-57 (1988)).

The term “vector” as used herein is intended to refer to a nucleic acidmolecule capable of transporting another nucleic acid to which it hasbeen linked. One type of vector is a “plasmid”, which refers to acircular double stranded DNA loop into which additional DNA segments maybe ligated. Other vectors include cosmids, bacterial artificialchromosomes (BAC) and yeast artificial chromosomes (YAC). Another typeof vector is a viral vector, wherein additional DNA segments may beligated into the viral genome (discussed in more detail below). Certainvectors are capable of autonomous replication in a host cell into whichthey are introduced (e.g., vectors having an origin of replication whichfunctions in the host cell). Other vectors can be integrated into thegenome of a host cell upon introduction into the host cell, and arethereby replicated along with the host genome. Moreover, certainpreferred vectors are capable of directing the expression of genes towhich they are operatively linked. Such vectors are referred to hereinas “recombinant expression vectors” (or simply, “expression vectors”).

“Operatively linked” expression control-sequences refers to a linkage inwhich the expression control sequence is contiguous with the gene ofinterest to control the gene of interest, as well as expression controlsequences that act in trans or at a distance to control the gene ofinterest.

The term “expression control sequence” as used herein refers topolynucleotide sequences which are necessary to affect the expression ofcoding sequences to which they are operatively linked. Expressioncontrol sequences are sequences which control the transcription,post-transcriptional events and translation of nucleic acid sequences.Expression control sequences include appropriate transcriptioninitiation, termination, promoter and enhancer sequences; efficient RNAprocessing signals such as splicing and polyadenylation signals;sequences that stabilize cytoplasmic mRNA; sequences that enhancetranslation efficiency (e.g., ribosome binding sites); sequences thatenhance protein stability; and when desired, sequences that enhanceprotein secretion. The nature of such control sequences differsdepending upon the host organism; in prokaryotes, such control sequencesgenerally include promoter, ribosomal binding site, and transcriptiontermination sequence. The term “control sequences” is intended toinclude, at a minimum, all components whose presence is essential forexpression, and can also include additional components whose presence isadvantageous, for example, leader sequences and fusion partnersequences.

The term “recombinant host cell” (or simply “host cell”), as usedherein, is intended to refer to a cell into which a recombinant vectorhas been introduced. It should be understood that such terms areintended to refer not only to the particular subject cell but to theprogeny of such a cell. Because certain modifications may occur insucceeding generations due to either mutation or environmentalinfluences, such progeny may not, in fact, be identical to the parentcell, but are still included within the scope of the term “host cell” asused herein. A recombinant host cell may be an isolated cell or cellline grown in culture or may be a cell which resides in a living tissueor organism.

The term “peptide” as used herein refers to a short polypeptide, e.g.,one that is typically less than about 50 amino acids long and moretypically less than about 30 amino acids long. The term as used hereinencompasses analogs and mimetics that mimic structural and thusbiological function.

The term “polypeptide” encompasses both naturally-occurring andnon-naturally-occurring proteins, and fragments, mutants, derivativesand analogs thereof. A polypeptide may be monomeric or polymeric.Further, a polypeptide may comprise a number of different domains eachof which has one or more distinct activities.

The term “isolated protein” or “isolated polypeptide” is a protein orpolypeptide that by virtue of its origin or source of derivation (1) isnot associated with naturally associated components that accompany it inits native state, (2) when it exists in a purity not found in nature,where purity can be adjudged with respect to the presence of othercellular material (e.g., is free of other proteins from the samespecies) (3) is expressed by a cell from a different species, or (4)does not occur in nature (e.g., it is a fragment of a polypeptide foundin nature or it includes amino acid analogs or derivatives not found innature or linkages other than standard peptide bonds). Thus, apolypeptide that is chemically synthesized or synthesized in a cellularsystem different from the cell from which it naturally originates willbe “isolated” from its naturally associated components. A polypeptide orprotein may also be rendered substantially free of naturally associatedcomponents by isolation, using protein purification techniques wellknown in the art. As thus defined, “isolated” does not necessarilyrequire that the protein, polypeptide, peptide or oligopeptide sodescribed has been physically removed from its native environment.

The term “polypeptide fragment” as used herein refers to a polypeptidethat has an amino-terminal and/or carboxy-terminal deletion compared toa full-length polypeptide. In a preferred embodiment, the polypeptidefragment is a contiguous sequence in which the amino acid sequence ofthe fragment is identical to the corresponding positions in thenaturally-occurring sequence. Fragments typically are at least 5, 6, 7,8, 9 or 10 amino acids long, preferably at least 12, 14, 16 or 18 aminoacids long, more preferably at least 20 amino acids long, morepreferably at least 25, 30, 35, 40 or 45, amino acids, even morepreferably at least 50 or 60 amino acids long, and even more preferablyat least 70 amino acids long.

A “modified derivative” refers to polypeptides or fragments thereof thatare substantially homologous in primary structural sequence but whichinclude, e.g., in vivo or in vitro chemical and biochemicalmodifications or which incorporate amino acids that are not found in thenative polypeptide. Such modifications include, for example,acetylation, carboxylation, phosphorylation, glycosylation,ubiquitination, labeling, e.g., with radionuclides, and variousenzymatic modifications, as will be readily appreciated by those wellskilled in the art. A variety of methods for labeling polypeptides andof substituents or labels useful for such purposes are well known in theart, and include radioactive isotopes such as ¹²⁵I, ³²P, ³⁵S, and ³H,ligands which bind to labeled antiligands (e.g., antibodies),fluorophores, chemiluminescent agents, enzymes, and antiligands whichcan serve as specific binding pair members for a labeled ligand. Thechoice of label depends on the sensitivity required, ease of conjugationwith the primer, stability requirements, and available instrumentation.Methods for labeling polypeptides are well known in the art. See Ausubelet al., 1992, hereby incorporated by reference.

The term “fusion protein” refers to a polypeptide comprising apolypeptide or fragment coupled to heterologous amino acid sequences.Fusion proteins are useful because they can be constructed to containtwo or more desired functional elements from two or more differentproteins. A fusion protein comprises at least 10 contiguous amino acidsfrom a polypeptide of interest, more preferably at least 20 or 30 aminoacids, even more preferably at least 40, 50 or 60 amino acids, yet morepreferably at least 75, 100 or 125 amino acids. Fusion proteins can beproduced recombinantly by constructing a nucleic acid sequence whichencodes the polypeptide or a fragment thereof in frame with a nucleicacid sequence encoding a different protein or peptide and thenexpressing the fusion protein. Alternatively, a fusion protein can beproduced chemically by crosslinking the polypeptide or a fragmentthereof to another protein.

The term “non-peptide analog” refers to a compound with properties thatare analogous to those of a reference polypeptide. A non-peptidecompound may also be termed a “peptide mimetic” or a “peptidomimetic”.See, e.g., Jones, (1992) Amino Acid and Peptide Synthesis, OxfordUniversity Press; Jung, (1997) Combinatorial Peptide and NonpeptideLibraries: A Handbook John Wiley; Bodanszky et al., (1993) PeptideChemistry—A Practical Textbook, Springer Verlag; “Synthetic Peptides: AUsers Guide”, G. A. Grant, Ed, W. H. Freeman and Co., 1992; Evans et al.J. Med. Chem. 30:1229 (1987); Fauchere, J. Adv. Drug Res. 15:29 (1986);Veber and Freidinger TINS p. 392 (1985); and references sited in each ofthe above, which are incorporated herein by reference. Such compoundsare often developed with the aid of computerized molecular modeling.Peptide mimetics that are structurally similar to useful peptides of theinvention may be used to produce an equivalent effect and are thereforeenvisioned to be part of the invention.

A “polypeptide mutant” or “mutein” refers to a polypeptide whosesequence contains an insertion, duplication, deletion, rearrangement orsubstitution of one or more amino acids compared to the amino acidsequence of a native or wild type protein. A mutein may have one or moreamino acid point substitutions, in which a single amino acid at aposition has been changed to another amino acid, one or more insertionsand/or deletions, in which one or more amino acids are inserted ordeleted, respectively, in the sequence of the naturally-occurringprotein, and/or truncations of the amino acid sequence at either or boththe amino or carboxy termini. A mutein may have the same but preferablyhas a different biological activity compared to the naturally-occurringprotein. For instance, a mutein may have an increased or decreasedneuron or NgR binding activity. In a preferred embodiment of the presentinvention, a MAG derivative that is a mutein (e.g., in MAG Ig-likedomain 5) has decreased neuronal growth inhibitory activity compared toendogenous or soluble wild-type MAG.

A mutein has at least 70% overall sequence homology to its wild-typecounterpart. Even more preferred are muteins having 80%, 85% or 90%overall sequence homology to the wild-type protein. In an even morepreferred embodiment, a mutein exhibits 95% sequence identity, even morepreferably 97%, even more preferably 98% and even more preferably 99%overall sequence identity. Sequence homology may be measured by anycommon sequence analysis algorithm, such as Gap or Bestfit.

Preferred amino acid substitutions are those which: (1) reducesusceptibility to proteolysis, (2) reduce susceptibility to oxidation,(3) alter binding affinity for forming protein complexes, (4) alterbinding affinity or enzymatic activity, and (5) confer or modify otherphysicochemical or functional properties of such analogs.

As used herein, the twenty conventional amino acids and theirabbreviations follow conventional usage. See Immunology—A Synthesis(2^(nd) Edition, E. S. Golub and D. R. Gren, Eds., Sinauer Associates,Sunderland, Mass. (1991)), which is incorporated herein by reference.Stereoisomers (e.g., D-amino acids) of the twenty conventional aminoacids, unnatural amino acids such as α-, α-disubstituted amino acids,N-alkyl amino acids, and other unconventional amino acids may also besuitable components for polypeptides of the present invention. Examplesof unconventional amino acids include: 4-hydroxyproline,γ-carboxyglutamate, ε-N,N,N-trimethyllysine, ε-N-acetyllysine,O-phosphoserine, N-acetylserine, N-formylmethionine, 3-methylhistidine,5-hydroxylysine, s-N-methylarginine, and other similar amino acids andimino acids (e.g., 4-hydroxyproline). In the polypeptide notation usedherein, the left-hand direction is the amino terminal direction and theright hand direction is the carboxy-terminal direction, in accordancewith standard usage and convention.

A protein has “homology” or is “homologous” to a second protein if thenucleic acid sequence that encodes the protein has a similar sequence tothe nucleic acid sequence that encodes the second protein.Alternatively, a protein has homology to a second protein if the twoproteins have “similar” amino acid sequences. (Thus, the term“homologous proteins” is defined to mean that the two proteins havesimilar amino acid sequences). In a preferred embodiment, a homologousprotein is one that exhibits 60% sequence homology to the wild typeprotein, more preferred is 70% sequence homology. Even more preferredare homologous proteins that exhibit 80%, 85% or 90% sequence homologyto the wild type protein. In a yet more preferred embodiment, ahomologous protein exhibits 95%, 97%, 98% or 99% sequence identity. Asused herein, homology between two regions of amino acid sequence(especially with respect to predicted structural similarities) isinterpreted as implying similarity in function.

When “homologous” is used in reference to proteins or peptides, it isrecognized that residue positions that are not identical often differ byconservative amino acid substitutions. A “conservative amino acidsubstitution” is one in which an amino acid residue is substituted byanother amino acid residue having a side chain (R group) with similarchemical properties (e.g., charge or hydrophobicity). In general, aconservative amino acid substitution will not substantially change thefunctional properties of a protein. In cases where two or more aminoacid sequences differ from each other by conservative substitutions, thepercent sequence identity or degree of homology may be adjusted upwardsto correct for the conservative nature of the substitution. Means formaking this adjustment are well known to those of skill in the art (see,e.g., Pearson et al., 1994, herein incorporated by reference).

The following six groups each contain amino acids that are conservativesubstitutions for one another: 1) Serine (S), Threonine (T); 2) AsparticAcid (D), Glutamic Acid (E); 3) Asparagine (N), Glutamine (Q); 4)Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine(M), Alanine (A), Valine (V), and 6) Phenylalanine (F), Tyrosine (Y),Tryptophan (W).

Sequence homology for polypeptides, which is also referred to as percentsequence identity, is typically measured using sequence analysissoftware. See, e.g., the Sequence Analysis Software Package of theGenetics Computer Group (GCG), University of Wisconsin BiotechnologyCenter, 910 University Avenue, Madison, Wis. 53705. Protein analysissoftware matches similar sequences using measure of homology assigned tovarious substitutions, deletions and other modifications, includingconservative amino acid substitutions. For instance, GCG containsprograms such as “Gap” and “Bestfit” which can be used with defaultparameters to determine sequence homology or sequence identity betweenclosely related polypeptides, such as homologous polypeptides fromdifferent species of organisms or between a wild type protein and amutein thereof. See, e.g., GCG Version 6.1.

A preferred algorithm when comparing a inhibitory molecule sequence to adatabase containing a large number of sequences from different organismsis the computer program BLAST (Altschul, S. F. et al. (1990) J. Mol.Biol. 215:403-410; Gish and States (1993) Nature Genet. 3:266-272;Madden, T. L. et al. (1996) Meth. Enzymol. 266:131-141; Altschul, S. F.et al. (1997) Nucleic Acids Res.25:3389-3402; Zhang, J. and Madden, T.L. (1997) Genome Res. 7:649-656), especially blastp or tblastn (Altschulet al., 1997). Preferred parameters for BLASTp are:

Expectation value:  10 (default) Filter: seg (default) Cost to open agap:  11 (default) Cost to extend a gap:  1 (default Max. alignments:100 (default) Word size:  11 (default) No. of descriptions: 100(default) Penalty Matrix: BLOWSUM62

The length of polypeptide sequences compared for homology will generallybe at least about 16 amino acid residues, usually at least about 20residues, more usually at least about 24 residues, typically at leastabout 28 residues, and preferably more than about 35 residues. Whensearching a database containing sequences from a large number ofdifferent organisms, it is preferable to compare amino acid sequences.Database searching using amino acid sequences can be measured byalgorithms other than blastp known in the art. For instance, polypeptidesequences can be compared using FASTA, a program in GCG Version 6.1.FASTA provides alignments and percent sequence identity of the regionsof the best overlap between the query and search sequences (Pearson,1990, herein incorporated by reference). For example, percent sequenceidentity between amino acid sequences can be determined using FASTA withits default parameters (a word size of 2 and the PAM250 scoring matrix),as provided in GCG Version 6.1, herein incorporated by reference.

“Specific binding” refers to the ability of two molecules to bind toeach other in preference to binding to other molecules in theenvironment. Typically, “specific binding” discriminates overadventitious binding in a reaction by at least two-fold, more typicallyby at least 10-fold, often at least 100-fold. Typically, the affinity oravidity of a specific binding reaction is at least about 10-7 M (e.g.,at least about 10⁻⁸ M or 10⁻⁹ M).

The term “region” as used herein refers to a physically contiguousportion of the primary structure of a biomolecule. In the case ofproteins, a region is defined by a contiguous portion of the amino acidsequence of that protein.

The term “domain” as used herein refers to a structure of a biomoleculethat contributes to a known or suspected function of the biomolecule.Domains may be co-extensive with regions or portions thereof; domainsmay also include distinct, non-contiguous regions of a biomolecule.Examples of protein domains include, but are not limited to, an Igdomain, an extracellular domain, a transmembrane domain, and acytoplasmic domain.

As used herein, the term “molecule” means any compound, including, butnot limited to, a small molecule, peptide, protein, sugar, nucleotide,nucleic acid, lipid, etc., and such a compound can be natural orsynthetic.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Exemplary methods andmaterials are described below, although methods and materials similar orequivalent to those described herein can also be used in the practice ofthe present invention and will be apparent to those of skill in the art.All publications and other references mentioned herein are incorporatedby reference in their entirety. In case of conflict, the presentspecification, including definitions, will control. The materials,methods, and examples are illustrative only and not intended to belimiting.

Throughout this specification and claims, the word “comprise” orvariations such as “comprises” or “comprising”, will be understood toimply the inclusion of a stated integer or group of integers but not theexclusion of any other integer or group of integers.

Engineering or Selecting Hosts with Modified Lipid-LinkedOligosaccharides for the Generation of Human-Like N-Glycans

The invention provides a method for producing a human-like glycoproteinin a non-human eukaryotic host cell. The method involves making or usinga non-human eukaryotic host cell diminished or depleted in an alg geneactivity (i.e., alg activities, including equivalent enzymaticactivities in non-fungal host cells) and introducing into the host cellat least one glycosidase activity. In a preferred embodiment, theglycosidase activity is introduced by causing expression of one or moremannosidase activities within the host cell, for example, by activationof a mannosidase activity, or by expression from a nucleic acid moleculeof a mannosidase activity, in the host cell.

In another embodiment, the method involves making or using a host celldiminished or depleted in the activity of one or more enzymes thattransfer a sugar residue to the 1,6 arm of lipid-linked oligosaccharideprecursors (FIG. 1). A host cell of the invention is selected for or isengineered by introducing a mutation in one or more of the genesencoding an enzyme that transfers a sugar residue (e.g., mannosylates)the 1,6 arm of a lipid-linked oligosaccharide precursor. The sugarresidue is more preferably mannose, is preferably a glucose, GlcNAc,galactose, sialic acid, fucose or GlcNAc phosphate residue. In apreferred embodiment, the activity of one or more enzymes thatmannosylate the 1,6 arm of lipid-linked oligosaccharide precursors isdiminished or depleted. The method may further comprise the step ofintroducing into the host cell at least one glycosidase activity (seebelow).

In yet another embodiment, the invention provides a method for producinga human-like glycoprotein in a non-human host, wherein the glycoproteincomprises an N-glycan having at least two GlcNAcs attached to atrimannose core structure.

In each above embodiment, the method is directed to making a host cellin which the lipid-linked oligosaccharide precursors are enriched inMan_(x)GlcNAc₂ structures, where X is 3, 4 or 5 (FIG. 2). Thesestructures are transferred in the ER of the host cell onto nascentpolypeptide chains by an oligosaccharyl-transferase and may then beprocessed by treatment with glycosidases (e.g., α-mannosidases) andglycosyltransferases (e.g., GnT1) to produce N-glycans havingGlcNAcMan_(x)GlcNAc₂ core structures, wherein X is 3, 4 or 5, and ispreferably 3 (FIGS. 2 and 3). As shown in FIG. 2, N-glycans having aGlcNAcMan_(x)GlcNAc₂ core structure where X is greater than 3 may beconverted to GlcNAcMan₃GlcNAc₂, e.g., by treatment with an α-1,3 and/orα-1,2-1,3 mannosidase activity, where applicable.

Additional processing of GlcNAcMan₃GlcNAc₂ by treatment withglycosyltransferases (e.g., GnTII) produces GlcNAc₂Man₃GlcNAc₂ corestructures which may then be modified, as desired, e.g., by ex vivotreatment or by heterologous expression in the host cell of a set ofglycosylation enzymes, including glycosyltransferases, sugartransporters and mannosidases (see below), to become human-likeN-glycans. Preferred human-like glycoproteins which may be producedaccording to the invention include those which comprise N-glycans havingseven or fewer, or three or fewer, mannose residues; comprise one ormore sugars selected from the group consisting of galactose, GlcNAc,sialic acid, and fucose; and comprise at least one oligosaccharidebranch comprising the structure NeuNAc-Gal-GlcNAc-Man.

In one embodiment, the host cell has diminished or depletedDol-P-Man:Man₅GlcNAc₂-PP-Dol Mannosyltransferase activity, which is anactivity involved in the first mannosylation step fromMan₅GlcNAc₂-PP-Dol to Man₆GlcNAc₂-PP-Dol at the luminal side of the ER(e.g., ALG3 FIG. 1; FIG. 2). In S. cerevisiae, this enzyme is encoded bythe ALG3 gene. As described above, S. cerevisiae cells harboring a leakyalg3-1 mutation accumulate Man₅GlcNAc₂-PP-Dol and cells having adeletion in alg3 appear to transfer Man₅GlcNAc₂ structures onto nascentpolypeptide chains within the ER. Accordingly, in this embodiment, hostcells will accumulate N-glycans enriched in Man₅GlcNAc₂ structures whichcan then be converted to GlcNAc₂Man₃GlcNAc₂ by treatment withglycosidases (e.g., with α-1,2 mannosidase, α-1,3 mannosidase orα-1,2-1,3 mannosidase activities (FIG. 2).

As described in Example 1, degenerate primers were designed based on analignment of Alg3 protein sequences from S. cerevisiae, D. melanogasterand humans (H. sapiens) (FIGS. 4 and 5), and were used to amplify aproduct from P. pastoris genomic DNA. The resulting PCR product was usedas a probe to identify and isolate a P. pastoris genomic clonecomprising an open reading frame (ORF) that encodes a protein having 35%overall sequence identity and 53% sequence similarity to the S.cerevisiae ALG3 gene (FIGS. 6 and 7). This P. pastoris gene is referredto herein as “PpALG3”. The ALG3 gene was similarly identified andisolated from K. lactis (Example 1; FIGS. 8 and 9).

Thus, in another embodiment, the invention provides an isolated nucleicacid molecule having a nucleic acid sequence comprising or consisting ofat least forty-five, preferably at least 50, more preferably at least 60and most preferably 75 or more nucleotide residues of the P. pastorisALG 3gene (FIG. 6) and the K. lactis ALG 3gene (FIG. 8), and homologs,variants and derivatives thereof. The invention also provides nucleicacid molecules that hybridize under stringent conditions to theabove-described nucleic acid molecules. Similarly, isolated polypeptides(including muteins, allelic variants, fragments, derivatives, andanalogs) encoded by the nucleic acid molecules of the invention areprovided (P. pastoris and K. lactis ALG 3gene products are shown inFIGS. 6 and 8). In addition, also provided are vectors, includingexpression vectors, which comprise a nucleic acid molecule of theinvention, as described further herein.

Using gene-specific primers, a construct was made to delete the PpALG3gene from the genome of P. pastoris (Example 1). This strain was used togenerate a host cell depleted in Dol-P-Man:Man₅GlcNAc₂-PP-DolMannosyltransferase activity and produce lipid-linked Man₅GlcNAc₂-PP-Dolprecursors which are transferred onto nascent polypeptide chains toproduce N-glycans having a Man₅GlcNAc₂ carbohydrate structure.

As described in Example 2, such a host cell may be engineered byexpression of appropriate mannosidases to produce N-glycans having thedesired Man₃GlcNAc₂ core carbohydrate structure. Expression of GnTs inthe host cell (e.g., by targeting a nucleic acid molecule or a libraryof nucleic acid molecules as described below) enables the modified hostcell to produce N-glycans having one or two GlcNAc structures attachedto each arm of the Man3 core structure (i.e., GlcNAc₁Man₃GlcNAc₂ orGlcNAc₂Man₃GlcNAc₂; see FIG. 3). These structures may be processedfurther using the methods of the invention to produce human-likeN-glycans on proteins which enter the secretion pathway of the hostcell.

In another embodiment, the host cell has diminished or depleteddolichyl-P-Man:Man₆GlcNAc2-PP-dolichyl α-1,2 mannosyltransferaseactivity, which is an α-1,2 mannosyltransferase activity involved in themannosylation step converting Man₆GlcNAc₂-PP-Dol to Man₇GlcNAc₂-PP-Dolat the luminal side of the ER (see above and FIGS. 1 and 2). In S.cerevisiae, this enzyme is encoded by the ALG9 gene. Cells harboring analg9 mutation accumulate Man₆GlcNAc₂-PP-Dol (FIG. 2) and transferMan₆GlcNAc₂ structures onto nascent polypeptide chains within the ER.Accordingly, in this embodiment, host cells will accumulate N-glycansenriched in Man₆GlcNAc₂ structures which can then be processed down tocore Man3 structures by treatment with α-1,2 and α-1,3 mannosidases (seeFIG. 3 and Examples 3 and 4).

A host cell in which the alg9 gene (or gene encoding an equivalentactivity) has been deleted is constructed (see, e.g., Example 3).Deletion of ALG9 (or ALG12; see below) creates a host cell whichproduces N-glycans with one or two additional mannoses, respectively, onthe 1,6 arm (FIG. 2). In order to make the 1,6 core-mannose accessibleto N-acetylglucosaminyltransferase II (GnTII) these mannoses have to beremoved by glycosidase(s). ER mannosidase typically will remove theterminal 1,2 mannose on the 1,6 arm and subsequently Mannosidase II(alpha 1-3,6 mannosidase) or other mannosidases such as alpha 1,2,alpha1,3 or alpha 1-2,3 mannosidases (e.g., from Xanthomonas manihotis;see Example 4) can act upon the 1,6 arm and subsequently GnTII cantransfer an N-acetylglucosamine, resulting in GlcNAc₂Man₃ (FIG. 2).

The resulting host cell, which is depleted for alg9p activity, isengineered to express α-1,2 and α-1,3 mannosidase activity (from one ormore enzymes, and preferably, by expression from a nucleic acid moleculeintroduced into the host cell and which expresses an enzyme targeted toa preferred subcellular compartment (see below). Example 4 describes thecloning and expression of one such enzyme from Xanthomonas manihotis.

In another embodiment, the host cell has diminished or depleteddolichyl-P-Man:Man7GlcNAc2-PP-dolichyl α-1,6 mannosyltransferaseactivity, which is an α-1,6 mannosyltransferase activity involved in themannosylation step converting Man₇GlcNAc₂-PP-Dol to Man₈GlcNAc₂-PP-Dol(which mannosylates the α-1,6 mannose on the 1,6 arm of the core mannosestructure) at the luminal side of the ER (see above and FIGS. 1 and 2).In S. cerevisiae, this enzyme is encoded by the ALG12 gene. Cellsharboring an alg12 mutation accumulate Man₇GlcNAc₂-PP-Dol (FIG. 2) andtransfer Man₇GlcNAc₂ structures onto nascent polypeptide chains withinthe ER. Accordingly, in this embodiment, host cells will accumulateN-glycans enriched in Man₇GlcNAc₂ structures which can then be processeddown to core Man3 structures by treatment with α-1,2 and α-1,3mannosidases (see FIG. 3 and Examples 3 and 4).

As described above for alg9 mutant hosts, the resulting host cell, whichis depleted for alg12p activity, is engineered to express α-1,2 andα-1,3 mannosidase activity (e.g., from one or more enzymes, andpreferably, by expression from one or more nucleic acid moleculesintroduced into the host cell and which express an enzyme activity whichis targeted to a preferred subcellular compartment (see below).

Engineering or Selecting Hosts Optionally Having Decreased Initiatingα-1,6 Mannosyltransferase Activity

In a preferred embodiment, the method of the invention involves makingor using a host cell which is both (a) diminished or depleted in theactivity of an alg gene or in one or more activities that mannosylateN-glycans on the α-1,6 arm of the Man₃GlcNAc₂ (“Man3”) core carbohydratestructure; and (b) diminished or depleted in the activity of aninitiating α-1,6-mannosyltransferase, i.e., an initiation specificenzyme that initiates outer chain mannosylation (on the α-1,3 arm of theMan3 cores structure). In S. cerevisiae, this enzyme is encoded by theOCH1 gene. Disruption of the och1 gene in S. cerevisiae results in aphenotype in which N-linked sugars completely lack the poly-mannoseouter chain. Previous approaches for obtaining mammalian-typeglycosylation in fungal strains have required inactivation of OCH1 (see,e.g., Chiba, 1998). Disruption of the initiatingα-1,6-mannosyltransferase activity in a host cell of the invention isoptional, however (depending on the selected host cell), as the Och1penzyme requires an intact Man₈GlcNAc for efficient mannose outer chaininitiation. Thus, the host cells selected or produced according to thisinvention, which accumulate lipid-linked oligosaccharides having sevenor fewer mannose residues will, after transfer, produce hypoglycosylatedN-glycans that will likely be poor substrates for Och1p (see, e.g.,Nakayama, 1997).

Engineering or Selecting Hosts Having Increased GlucosyltransferaseActivity

As discussed above, glucosylated oligosaccharides are thought to betransferred to nascent polypeptide chains at a much higher rate thantheir nonglucosylated counterparts. It appears that substraterecognition by the oligosaccharyltransferase complex is enhanced byaddition of glucose to the antennae of lipid-linked oligosaccharides. Itis thus desirable to create or select host cells capable of optimalglucosylation of the lipid-linked oligosaccharides. In such host cells,underglycosylation will be substantially decreased or even abolished,due to a faster and more efficient transfer of glucosylated Man₅structures onto the nascent polypeptide chain.

Accordingly, in another embodiment of the invention, the method isdirected to making a host cell in which the lipid-linked N-glycanprecursors are transferred efficiently to the nascent polypeptide chainin the ER. In a preferred embodiment, transfer is augmented byincreasing the level of glucosylation on the branches of lipid-linkedoligosaccharides which, in turn, will make them better substrates foroligosaccharyltransferase.

In one preferred embodiment, the invention provides a method for makinga human-like glycoprotein which uses a host cell in which one or moreenzymes responsible for glucosylation of lipid-linked oligosaccharidesin the ER has increased activity. One way to enhance the degree ofglucosylation of the lipid-linked oligosaccharides is to overexpress oneor more enzymes responsible for the transfer of glucose residues ontothe antennae of the lipid-linked oligosaccharide. In particular,increasing α-1,3 glucosyltransferase activity will increase the amountof glucosylated lipid-linked Man₅ structures and will reduce oreliminate the underglycosylation of secreted proteins. In S. cerevisiae,this enzyme is encoded by the ALG6 gene.

Saccharomyces cerevisiae ALG6 and its human counterpart have been cloned(Imbach, 1999; Reiss, 1996). Due to the evolutionary conservation of theearly steps of glycosylation, ALG6 loci are expected to be homologousbetween species and may be cloned based on sequence similarities byanyone skilled in the art. (The same holds true for cloning andidentification of ALG8 and ALG10 loci from different species.) Inaddition, different glucosyltransferases from different species can thenbe tested to identify the ones with optimal activities.

The introduction of additional copies of an ALG6 gene and/or theexpression of ALG6 under the control of a strong promoter, such as theGAPDH promoter, is one of several ways to increase the degree ofglucosylated lipid-linked oligosaccharides. The ALG6 gene from P.pastoris is cloned and expressed (Example 5). ALG6 nucleic acid andamino acid sequences are show in FIG. 25 (S. cerevisiae) and FIG. 26 (P.pastoris). These sequences are compared to other eukaryotic ALG6sequences in FIG. 27.

Accordingly, another embodiment of the invention provides a method toenhance the degree of glucosylation of lipid-linked oligosaccharidescomprising the step of increasing alpha-1,3 glucosyltransferase activityin a host cell. The increase in activity may be achieved byoverexpression of nucleic acid sequences encoding the activity, e.g., byoperatively linking the nucleic acid encoding the activity with one ormore heterologous expression control sequences. Preferred expressioncontrol sequences include transcription initiation, termination,promoter and enhancer sequences; RNA splice donor and polyadenylationsignals; mRNA stabilizing sequences; ribosome binding sites; proteinstabilizing sequences; and protein secretion sequences.

In another embodiment, the increase in alpha-1,3 glucosyltransferaseactivity is achieved by introducing a nucleic acid molecule encoding theactivity on a multi-copy plasmid, using techniques well known to theskilled worker. In yet another embodiment, the degree of glucosylationof lipid-linked oligosaccharides comprising decreasing the substratespecificity of oligosaccharyl transferase activity in a host cell. Thisis achieved by, for example, subjecting at least one nucleic acidencoding the activity to a technique such as gene shuffling, in vitromutagenesis, and error-prone polymerase chain reaction, all of which arewell-known to one of skill in the art. Naturally, ALG8 and ALG10 can beoverexpressed in a host cell and tested in a similar fashion.

Accordingly, in a preferred embodiment, the invention provides a methodfor making a human-like glycoprotein using a host cell which isengineered or selected so that one or more enzymes responsible forglucosylation of lipid-linked oligosaccharides in the ER has increasedactivity. In a more preferred embodiment, the invention uses a host cellhaving both (a) diminished or depleted in the activity of one or morealg gene activities or activities that mannosylate N-glycans on theα-1,6 arm of the Man₃GlcNAc₂ (“Man3”) core carbohydrate structure and(b) engineered or selected so that one or more enzymes responsible forglucosylation of lipid-linked oligosaccharides in the ER has increasedactivity. The lipid-linked Man₅ structure found in an alg3 mutantbackground, however, is not a preferred substrate for Alg6p.Accordingly, the skilled worker may identify Alg6p, Alg8p and Alg10pwith an increased substrate specificity (Gibbs, 2001) e.g., bysubjecting nucleic acids encoding such enzymes to one or more rounds ofgene shuffling, error prone PCR, or in vitro mutagenesis approaches andselecting for increased substrate specificity in a host cell ofinterest, using molecular biology and genetic selection techniques wellknown to those of skill in the art. It will be appreciated by theskilled worker that such techniques for improving enzyme substratespecificities in a selected host strain are not limited to thisparticular embodiment of the invention but rather, may be used in anyembodiment to optimize further the production of human-like N-glycans ina non-human host cell.

As described, once Man₅ is transferred onto the nascent polypeptidechain, expression of suitable α-1,2-mannosidase(s), as provided by thepresent invention, will further trim Man₅GlcNAc₂ structures to yield thedesired core Man₃GlcNAc₂ structures. α-1,2-mannosidases remove onlyterminal α-1,2-linked mannose residues and are expected to recognize theMan₅GlcNAc₂-Man₇GlcNAc₂ specific structures made in alg3, 9 and 12mutant host cells and in host cells in which homologs to these genes aremutated.

As schematically presented in FIG. 3, co-expression of appropriateUDP-sugar-transporter(s) and -transferase(s) will cap the terminal α-1,6and α-1,3 residues with GlcNAc, resulting in the necessary precursor formammalian-type complex and hybrid N-glycosylation: GlcNAc₂Man₅GlcNAc₂.The peptide-bound N-linked oligosaccharide chain GlcNAc₂Man₃GlcNAc₂(FIG. 3) then serves as a precursor for further modification to amammalian-type oligosaccharide structure. Subsequent expression ofgalactosyl-tranferases and genetically engineering the capacity totransfer sialylic acid will produce a mammalian-type (e.g., human-like)N-glycan structure.

A desired host cell according to the invention can be engineered oneenzyme or more than one enzyme at a time. In addition, a library ofgenes encoding potentially useful enzymes can be created, and a strainhaving one or more enzymes with optimal activities or producing the most“human-like” glycoproteins, selected by transforming target host cellswith one or more members of the library. Lower eukaryotes that are ableto produce glycoproteins having the core N-glycan Man₃GlcNAc₂ areparticularly useful because of the ease of performing geneticmanipulations, and safety and efficiency features. In a preferredembodiment, at least one further glycosylation reaction is performed, exvivo or in vivo, to produce a human-like N-glycan. In a more preferredembodiment, active forms of glycosylating enzymes are expressed in theendoplasmic reticulum and/or Golgi apparatus of the host cell to producethe desired human-like glycoprotein.

Host Cells

A preferred non-human host cell of the invention is a lower eukaryoticcell, e.g., a unicellular or filamentous fungus, which is diminished ordepleted in the activity of one or more alg gene activities (includingan enzymatic activity which is a homolog or equivalent to an algactivity). Another preferred host cell of the invention is diminished ordepleted in the activity of one or more enzymes (other than algactivities) that mannosylate the α-1,6 arm of a lipid-linkedoligosaccharide structure.

While lower eukaryotic host cells are preferred, a wide variety of hostcells having the aforementioned properties are envisioned as beinguseful in the methods of the invention. Plant cells, for instance, maybe engineered to express a human-like glycoprotein according to theinvention. Likewise, a variety of non-human, mammalian host cells may bealtered to express more human-like glycoproteins using the methods ofthe invention. An appropriate host cell can be engineered, or one of themany such mutants already described in yeasts may be used. A preferredhost cell of the invention, as exemplified herein, is ahypermannosylation-minus (OCH1) mutant in Pichia pastoris which hasfurther been modified to delete the alg3 gene. Other preferred hosts arePichia pastoris mutants having och1 and alg 9 or alg12 mutations.

Formation of Complex N-Glycans

The sequential addition of sugars to the modified, nascent N-glycanstructure involves the successful targeting of glucosyltransferases intothe Golgi apparatus and their successful expression. This processrequires the functional expression, e.g., of GnT I, in the early ormedial Golgi apparatus as well as ensuring a sufficient supply ofUDP-GlcNAc (e.g., by expression of a UDP-GlcNAc transporter).

To characterize the glycoproteins and to confirm the desiredglycosylation, the glycoproteins were purified, the N-glycans werePNGase-F released and then analyzed by MALDI-TOF-MS (Example 2). Kringle3 domain of human plasminogen was used as the reporter protein. Thissoluble glycoprotein was produced in P. pastoris in an alg3, och1knockout background (Example 2).

GlcNAcMan₅GlcNAc₂ was produced as the predominant N-glycan afteraddition of human GnT I, and K. lactis UDP-GlcNAc transporter in FIG. 16(Example 2). The mass of this N-glycan is consistent with the mass ofGlcNAcMan₅GlcNAc₂ at 1463 (m/z). To confirm the addition of the GlcNAconto Man₅GlcNAc₂, a β-N-hexosaminidase digest was performed, whichrevealed a peak at 1260 (m/z), consistent with the mass of Man₅GlcNAc₂(FIG. 17).

The N-glycans from the alg3 och1 deletion in one strain PBP3 (Example 2)provided two distinct peaks at 1138 (m/z) and 1300 (m/z), which isconsistent with structures GlcNAcMan₃GlcNAc₂ and GlcNAcMan₄GlcNAc₂ (FIG.18). After an in vitro α1,2-mannosidase digestion for redundantmannoses, a peak eluted at 1138 (m/z), which is consistent withGlcNAcMan₃GlcNAc₂ (FIG. 19). To confirm the addition of the GlcNAc ontothe Man₃GlcNAc₂ structure, a β-N-hexosaminidase digest was performed,which revealed a peak at 934 (m/z), consistent with the mass ofMan₃GlcNAc₂ (FIG. 20).

The addition of the second GlcNAc onto GlcNAcMan₃GlcNAc₂ is shown inFIG. 21. The peak at 1357 (m/z) corresponds to GlcNAc₂Man₃GlcNAc₂. Toconfirm the addition of the two GlcNAcs onto the core mannose structureMan₃GlcNAc₂, another β-N-hexosaminidase digest was performed, whichrevealed a peak at 934 (m/z), consistent with the mass of Man₃GlcNAc₂(FIG. 22). This is conclusive data displaying a complex-typeglycoprotein made in yeast cells.

The in vitro addition of UDP-galactose and β1,4-galactosyltransferaseonto the GlcNAc₂Man₃GlcNAc₂ resulted in a peak at 1664 (m/z), which isconsistent with the mass of Gal₂GlcNAc₂Man₃GlcNAc₂ (FIG. 23) Finally,the in vitro addition of CMP-N-acetylneuraminic acid andsialyltransferase resulted in a peak at 2248 (m/z), which is consistentwith the mass of NANA₂Gal₂GlcNAc₂Man₃GlcNAC₂ (FIG. 24). The above datasupports the use of non-mammalian host cells, which are capable ofproducing complex human-like glycoproteins.

Targeting of Glycosyl- and Galactosyl-Transferases to SpecificOrganelles.

Much work has been dedicated to revealing the exact mechanism by whichthese enzymes are retained and anchored to their respective organelle.Although complex, evidence suggests that, stem region, membrane spanningregion and cytoplasmic tail individually or in concert direct enzymes tothe membrane of individual organelles and thereby localize theassociated catalytic domain to that locus.

The method by which active glycosyltransferases can be expressed anddirected to the appropriate organelle such that a sequential order ofreactions may occur, that leads to complex N-glycan formation, is asfollows:

(A) Establish a DNA library of regions that are known to encodeproteins/peptides that mediate localization to a particular location inthe secretory pathway (ER, Golgi and trans Golgi network). A limitedselection of such enzymes and their respective location is shown inTable 1. These sequences may be selected from the host to be engineeredas well as other related or unrelated organism. Generally such sequencesfall into three categories: (1) N-terminal sequences encoding acytosolic tail (ct), a transmembrane domain (tmd) and part of a somewhatmore ambiguously defined stem region (sr), which together orindividually anchor proteins to the inner (lumenal) membrane of theGolgi, (2) retrieval signals which are generally found at the C-terminussuch as the HDEL or KDEL tetrapeptide, and (3) membrane spanningnucleotide sugar transporters, which are known to locate in the Golgi.In the first case, where the localization region consists of variouselements (ct, tmd and sr) the library is designed such that the ct, thetmd and various parts of the stem region are represented. This may beaccomplished by using PCR primers that bind to the 5′ end of the DNAencoding the cytosolic region and employing a series of opposing primersthat bind to various parts of the stem region. In addition one wouldcreate fusion protein constructs that encode sugar nucleotidetransporters and known retrieval signals.(B) A second step involves the creation of a series of fusion proteinconstructs, that encode the above mentioned localization sequences andthe catalytic domain of a particular glycosyltransferase cloned in frameto such localization sequence (e.g. GnT I, GalT, Fucosyltransferase orST). In the case of a sugar nucleotide transporter fused to a catalyticdomain one may design such constructs such that the catalytic domain(e.g. GnT I) is either at the N- or the C-terminus of the resultingpolypeptide. The catalytic domain, like the localization sequence, maybe derived from various different sources. The choice of such acatalytic domains may be guided by the knowledge of the particularenvironment in which the catalytic domain is to be active. For example,if a particular glycosyltransferase is to be active in the late Golgi,and all known enzymes of the host organism in the late Golgi have a pHoptimum of 7.0, or the late Golgi is known to have a particular pH, onewould try to select a catalytic domain that has maximum activity at thatpH. Existing in vivo data on the activity of such enzymes, in particularhosts, may also be of use. For example, Schwientek and coworkers showedthat GalT activity can be engineered into the Golgi of S. cerevisiae andshowed that such activity was present by demonstrating the transfer ofsome Gal to existing GlcNAc₂ in an alg mutant of S. cerevisiae. Inaddition, one may perform several rounds of gene shuffling or errorprone PCR to obtain a larger diversity within the pool of fusionconstructs, since it has been shown that single amino mutations maydrastically alter the activity of glycoprotein processing enzymes(Romero et al., 2000). Full length sequences of glycosyltransferases andtheir endogenous anchoring sequence may also be used. In a preferredembodiment, such localization/catalytic domain libraries are designed toincorporate existing information on the sequential nature ofglycosylation reactions in higher eukaryotes. In other words, reactionsknown to occur early in the course of glycoprotein processing requirethe targeting of enzymes that catalyze such reactions to an early partof the Golgi or the ER. For example, the trimming of Man₈GlcNAc₂ toMan₅GlcNAc₂ is an early step in complex N-glycan formation. Sinceprotein processing is initiated in the ER and then proceeds through theearly, medial and late Golgi, it is desirable to have this reactionoccur in the ER or early Golgi. When designing a library for mannosidaseI localization, one thus attempts to match ER and early Golgi targetingsignals with the catalytic domain of mannosidase I.

Upon transformation of the host strain with the fusion construct librarya selection process is used to identify which particular combination oflocalization sequence and catalytic domain in fact have the maximumeffect on the carbohydrate structure found in such host strain. Suchselection can be based on any number of assays or detection methods.They may be carried out manually or may be automated through the use ofhigh throughput screening equipment.

In another example, GnT I activity is required for the maturation ofcomplex N-glycans, because only after addition of GlcNAc to the terminalα1,3 mannose residue may further trimming of such a structure to thesubsequent intermediate GlcNAcMan₃GlcNAc₂ structure occur. MannosidaseII is most likely not capable of removing the terminal α1,3- andα1,6-mannose residues in the absence of a terminal β1,2-GlcNAc and thusthe formation of complex N-glycans will not proceed in the absence ofGnT I activity (Schachter, 1991). Alternatively, one may first engineeror select a strain that makes sufficient quantities of Man₅GlcNAc₂ asdescribed in this invention by engineering or selecting a straindeficient in Alg3P activity. In the presence of sufficient UDP-GlcNActransporter activity, as may be achieved by engineering or selecting astrain that has such UDP-GlcNAc transporter activity, GlcNAc can beadded to the terminal α-1,3 residue by GnTI as in vitro a Man₃ structureis recognized by by rat liver GnTI (Moller, 1992).

In another approach, one may incorporate the expression of a UDP-GlcNActransporter into the library mentioned above such that the desiredconstruct will contain: (1) a region by which the transformed constructis maintained in the cell (e.g. origin of replication or a region thatmediates chromosomal integration), (2) a marker gene that allows for theselection of cells that have been transformed, includingcounterselectable and recyclable markers such as ura3 or T-urf13(Soderholm, 2001) or other well characterized selection-markers (e.g.his4, bla, Sh ble etc.), (3) a gene encoding a UDP-GlcNAc transporter(e.g. from K. lactis, (Abeijon, 1996), or from H. sapiens (Ishida,1996), and (4) a promotor activating the expression of the abovementioned localization/catalytic domain fusion construct library.

After transformation of the host with the library of fusion constructsdescribed above, one may screen for those cells that have the highestconcentration of terminal GlcNAc on the cell surface, or secrete theprotein with the highest terminal GlcNAc content. Such a screen may bebased on a visual method, like a staining procedure, the ability to bindspecific terminal GlcNAc binding antibodies or lectins conjugated to amarker (such lectins are available from E.Y. Laboratories Inc., SanMateo, Calif.), the reduced ability of specific lectins to bind toterminal mannose residues, the ability to incorporate a radioactivelylabeled sugar in vitro, altered binding to dyes or charged surfaces, ormay be accomplished by using a Fluorescence Assisted Cell Sorting (FACS)device in conjunction with a fluorophore labeled lectin or antibody(Guillen, 1998). It may be advantageous to enrich particular phenotypeswithin the transformed population with cytotoxic lectins. U.S. Pat. No.5,595,900 teaches several methods by which cells with a desiredextra-cellular carbohydrate structures may be identified. Repeatedlycarrying out this strategy allows for the sequential engineering of moreand more complex glycans in lower eukaryotes.

After transformation, one may select for transformants that allow forthe most efficient transfer of GlcNAc by GlcNAc Transferase II fromUDP-GlcNAc in an in vitro assay. This screen may be carried out bygrowing cells harboring the transformed library under selective pressureon an agar plate and transferring individual colonies into a 96-wellmicrotiter plate. After growing the cells, the cells are centrifuged,the cells resuspended in buffer, and after addition of UDP-GlcNAc andGnT V, the release of UDP is determined either by HPLC or an enzymelinked assay for UDP. Alternatively, one may use radioactively labeledUDP-GlcNAc and GnT V, wash the cells and then look for the release ofradioactive GlcNAc by N-actylglucosaminidase. All this may be carriedmanually or automated through the use of high throughput screeningequipment.

Transformants that release more UDP, in the first assay, or moreradioactively labeled GlcNAc in the second assay, are expected to have ahigher degree of GlcNAcMan₃GlcNAc₂ (FIG. 3) on their surface and thusconstitute the desired phenotype. Alternatively, one may any use anyother suitable screen such as a lectin binding assay that is able toreveal altered glycosylation patterns on the surface of transformedcells. In this case the reduced binding of lectins specific to terminalmannoses may be a suitable selection tool. Galantus nivalis lectin bindsspecifically to terminal a-1,3 mannose, which is expected to be reducedif sufficient mannsosidase II activity is present in the Golgi. One mayalso enrich for desired transformants by carrying out a chromatographicseparation step that allows for the removal of cells containing a highterminal mannose content. This separation step would be carried out witha lectin column that specifically binds cells with a high terminalmannose content (e.g Galantus nivalis lectin bound to agarose, SIGMA®,St. Louis, Mo.) over those that have a low terminal mannose content. Inaddition, one may directly create such fusion protein constructs, asadditional information on the localization of active carbohydratemodifying enzymes in different lower eukaryotic hosts becomes availablein the scientific literature. For example, the prior art teaches us thathuman beta 1,4-GalTr can be fused to the membrane domain of MNT, amannosyltransferase from S. cerevisiae, and localized to the Golgiapparatus while retaining its catalytic activity (Schwientek et al.,1995), If S. cerevisiae or a related organism is the host to beengineered one may directly incorporate such findings into the overallstrategy to obtain complex N-glycans from such a host. Several such genefragments in P. pastoris have been identified that are related toglycosyltransferases in S. cerevisiae and thus could be used for thatpurpose.

TABLE 1 Gene or Location of gene sequence Organism Function product MnsIS. cerevisiae mannosidase ER Och1 S. cerevisiae 1,6-mannosyltransferaseGolgi (cis) Mnn2 S. cerevisiae 1,2-mannosyltransferase Golgi (medial)Mnn1 S. cerevisiae 1,3-mannosyltransferase Golgi (trans) Och1 P.pastoris 1,6-mannosyltransferase Golgi (cis) 2,6 ST H. sapiens2,6-sialyltransferase trans-Golgi S. frugiperda network β1,4 Gal Tbovine milk UDP-Gal transporter Golgi Mnt1 S. cerevisiae1,2-mannosyltransferase Golgi (cis) HDEL at C- S. cerevisiae retrievalsignal ER terminusIntegration Sites

As one ultimate goal of this genetic engineering effort is a robustprotein production strain that is able to perform well in an industrialfermentation process, the integration of multiple genes into the host(e.g., fungal) chromosome involves careful planning. The engineeredstrain will most likely have to be transformed with a range of differentgenes, and these genes will have to be transformed in a stable fashionto ensure that the desired activity is maintained throughout thefermentation process. Any combination of the following enzyme activitieswill have to be engineered into the fungal protein expression host:sialyltransferases, mannosidases, fucosyltransferases,galactosyltransferases, glucosyltransferases, GlcNAc transferases, ERand Golgi specific transporters (e.g. syn and antiport transporters forUDP-galactose and other precursors), other enzymes involved in theprocessing of oligosaccharides, and enzymes involved in the synthesis ofactivated oligosaccharide precursors such as UDP-galactose,CMP-N-acetylneuraminic acid. At the same time, a number of genes whichencode enzymes known to be characteristic of non-human glycosylationreactions, will have to be deleted. Such genes and their correspondingproteins have been extensively characterized in a number of lowereukaryotes (e.g. S. cerevisiae, T. reesei, A. nidulans etc.), therebyproviding a list of known glycosyltransferases in lower eukaryotes,their activities and their respective genetic sequence. These genes arelikely to be selected from the group of mannosyltransferases e.g. 1,3mannosyltransferases (e.g. MNN1 in S. cerevisiae) (Graham, 1991), 1,2mannosyltransferases (e.g. KTR/KRE family from S. cerevisiae), 1,6mannosyltransferases (OCH1 from S. cerevisiae), mannosylphosphatetransferases (MNN4 and MNN6 from S. cerevisiae) and additional enzymesthat are involved in aberrant i.e. non human glycosylation reactions.Many of these genes have in fact been deleted individually giving riseto viable phenotypes with altered glycosylation profiles. Examples areshown in Table 2:

TABLE 2 Structure wild Structure Strain Mutant type mutant AuthorsSchizosaccharomyces OCH1 Mannan (i.e. Man₈GlcNAc₂ Yoko-o et al., 2001pombe Man_(>9)GlcNAc₂) S. cerevisiae OCH1, Mannan (i.e. Man₈GlcNAc₂Nakanishi-Shindo MNN1 Man_(>9)GlcNAc₂) et al,. 1993 S. cerevisiae OCH1,Mannan (i.e. Man₈GlcNAc₂ Chiba et al., 1998 MNN1, Man_(>9)GlcNAc₂) MNN4As any strategy to engineer the formation of complex N-glycans into alower eukaryote involves both the elimination as well as the addition ofglycosyltransferase activities, a comprehensive scheme will attempt tocoordinate both requirements. Genes that encode enzymes that areundesirable serve as potential integration sites for genes that aredesirable. For example, 1,6 mannosyltransferase activity is a hallmarkof glycosylation in many known lower eukaryotes. The gene encodingalpha-1,6 mannosyltransferase (OCH1) has been cloned from S. cerevisiaeand mutations in the gene give raise to a viable phenotype with reducedmannosylation. The gene locus encoding alpha-1,6 mannosyltransferaseactivity therefor is a prime target for the integration of genesencoding glycosyltransferase activity. In a similar manner, one canchoose a range of other chromosomal integration sites that, based on agene disruption event in that locus, are expected to: (1) improve thecells ability to glycosylate in a more human like fashion, (2) improvethe cells ability to secrete proteins, (3) reduce proteolysis of foreignproteins and (4) improve other characteristics of the process thatfacilitate purification or the fermentation process itself.Providing Sugar Nucleotide Precursors

A hallmark of higher eukaryotic glycosylation is the presence ofgalactose, fucose, and a high degree of terminal sialic acid onglycoproteins. These sugars are not generally found on glycoproteinsproduced in yeast and filamentous fungi and the method discussed aboveallows for the engineering of strains that localize glycosyltransferasein the desired organelle. Formation of complex N-glycan synthesis is asequential process by which specific sugar residues are removed andattached to the core oligosaccharide structure. In higher eukaryotes,this is achieved by having the substrate sequentially exposed to variousprocessing enzymes. These enzymes carry out specific reactions dependingon their particular location within the entire processing cascade. This“assembly line” consists of ER, early, medial and late Golgi, and thetrans Golgi network all with their specific processing environment. Torecreate the processing of human glycoproteins in the Golgi and ER oflower eukaryotes, numerous enzymes (e.g. glycosyltransferases,glycosidases, phosphatases and transporters) have to be expressed andspecifically targeted to these organelles, and preferably, in a locationso that they function most efficiently in relation to their environmentas well as to other enzymes in the pathway.

Several individual glycosyltransferases have been cloned and expressedin S. cerevisiae (GalT, GnT I), Aspergillus nidulans (GnT I) and otherfungi, without however demonstrating the desired outcome of“humanization” on the glycosylation pattern of the organisms (Yoshida,1995; Schwientek, 1995; Kalsner, 1995). It was speculated that thecarbohydrate structure required to accept sugars by the action of suchglycosyltransferases was not present in sufficient amounts. While thismost likely contributed to the lack of complex N-glycan formation, thereare currently no reports of a fungus supplying a Man₅GlcNAc₂ structure,having GnT I activity and having UDP-Gn transporter activity engineeredinto the fungus. It is the combination of these three biochemical eventsthat are required for hybrid and complex N-glycan formation.

In humans, the full range of nucleotide sugar precursors (e.g.UDP-N-acetylglucosamine, UDP-N-acetylgalactosamine,CMP-N-acetylneuraminic acid, UDP-galactose, etc.) are generallysynthesized in the cytosol and transported into the Golgi, where theyare attached to the core oligosaccharide by glycosyltransferases. Toreplicate this process in lower eukaryotes, sugar nucleoside specifictransporters have to be expressed in the Golgi to ensure adequate levelsof nucleoside sugar precursors (Sommers, 1981; Sommers, 1982; Perez,1987). A side product of this reaction is either a nucleosidediphosphate or monophosphate. While monophosphates can be directlyexported in exchange for nucleoside triphosphate sugars by an antiportmechanism, diphospho nucleosides (e.g. GDP) have to be cleaved byphosphatases (e.g. GDPase) to yield nucleoside monophosphates andinorganic phosphate prior to being exported. This reaction appears to beimportant for efficient glycosylation, as GDPase from S. cerevisiae hasbeen found to be necessary for mannosylation. However, the enzyme onlyhas 10% of the activity towards UDP (Berninsone, 1994). Lower eukaryotesoften do not have UDP specific diphosphatase activity in the Golgi sincethey do not utilize UDP-sugar precursors for glycoprotein synthesis inthe Golgi.

Schizosaccharomyces pombe, a yeast found to add galactose residues tocell wall polysaccharides (from UDP-galactose) was found to havespecific UDPase activity further suggesting the requirement for such anenzyme (Berninsone et al., 1994). UDP is known to be a potent inhibitorof glycosyltransferases and the removal of this glycosylation sideproduct is important in order to prevent glycosyltransferase inhibitionin the lumen of the Golgi (Khatara et al., 1974). Thus, one may need toprovide for the removal of UDP, which is expected to accumulate in theGolgi of such an engineered strains (Beminsone, 1995; Beaudet, 1998).

In another example, 2,3 sialyltransferase and 2,6 sialyltransferase capgalactose residues with sialic acid in the trans-Golgi and TGN of humansleading to a mature form of the glycoprotein. To reengineer thisprocessing step into a metabolically engineered yeast or fungus willrequire (1) 2,3-sialyltransferase activity and (2) a sufficient supplyof CMP-N-acetyl neuraminic acid, in the late Golgi of yeast. To obtainsufficient 2,3-sialyltransferase activity in the late Golgi, thecatalytic domain of a known sialyltransferase (e.g. from humans) has tobe directed to the late Golgi in fungi (see above). Likewise,transporters have to be engineered to that allow the transport ofCMP-N-acetyl neuraminic acid into the late Golgi. There is currently noindication that fungi synthesize sufficient amounts of CMP-N-acetylneuraminic acid, not to mention the transport of such a sugar-nucleotideinto the Golgi. Consequently, to ensure the adequate supply of substratefor the corresponding glycosyltransferases, one has to metabolicallyengineer the production of CMP-sialic acid into the fungus.

Methods for Providing Sugar Nucleotide Precursors to the GolgiApparatus:

UDP-N-acetyl-glucosamine

The cDNA of human UDP-N-acetylglucosamine transporter, which wasrecognized through a homology search in the expressed sequence tagsdatabase (dbEST) was cloned by Ishida and coworkers (Ishida, 1999).Guillen and coworkers have cloned the mammalian Golgi membranetransporter for UDP-N-acetylglucosamine by phenotypic correction withcDNA from canine kidney cells (MDCK) of a recently characterizedKluyveromyces lactis mutant deficient in Golgi transport of the abovenucleotide sugar (Guillen, 1998). Their results demonstrate that themammalian Golgi UDP-GlcNAc transporter gene has all of the necessaryinformation for the protein to be expressed and targeted functionally tothe Golgi apparatus of yeast and that two proteins with very differentamino acid sequences may transport the same solute within the same Golgimembrane (Guillen, 1998).

GDP-Fucose

The rat liver Golgi membrane GDP-fucose transporter has been identifiedand purified by Puglielli, L. and C. B. Hirschberg (Puglielli, 1999).The corresponding gene has not been identified however N-terminalsequencing can be used for the design of oligonucleotide probes specificfor the corresponding gene. These oligonucleotides can be used as probesto clone the gene encoding for GDP-fucose transporter.

UDP-Galactose

Two heterologous genes, gma12(+) encoding alpha1,2-galactosyltransferase (alpha 1,2 GalT) from Schizosaccharomycespombe and (hUGT2) encoding human UDP-galactose (UDP-Gal) transporter,have been functionally expressed in S. cerevisiae to examine theintracellular conditions required for galactosylation. Correlationbetween protein galactosylation and UDP-galactose transport activityindicated that an exogenous supply of UDP-Gal transporter, rather thanalpha 1,2 GalT played a key role for efficient galactosylation in S.cerevisiae (Kainuma, 1999). Likewise a UDP-galactose transporter from S.pombe was cloned (Aoki, 1999; Segawa, 1999).

CMP-N-acetylneuraminic acid (CMP-Sialic Acid)

Human CMP-sialic acid transporter (hCST) has been cloned and expressedin Lec 8 CHO cells (Aoki, 1999; Eckhardt, 1997). The functionalexpression of the murine CMP-sialic acid transporter was achieved inSaccharomyces cerevisiae (Beminsone, 1997). Sialic acid has been foundin some fungi, however it is not clear whether the chosen host systemwill be able to supply sufficient levels of CMP-Sialic acid. Sialic acidcan be either supplied in the medium or alternatively fungal pathwaysinvolved in sialic acid synthesis can also be integrated into the hostgenome.

Diphosphatases

When sugars are transferred onto a glycoprotein, either a nucleosidediphosphate or monophosphate, is released from the sugar nucleotideprecursors. While monophosphates can be directly exported in exchangefor nucleoside triphosphate sugars by an antiport mechanism, diphosphonucleosides (e.g. GDP) have to be cleaved by phosphatases (e.g. GDPase)to yield nucleoside monophosphates and inorganic phosphate prior tobeing exported. This reaction appears to be important for efficientglycosylation, as GDPase from S. cerevisiae has been found to benecessary for mannosylation. However, the enzyme only has 10% of theactivity towards UDP (Berninsone, 1994). Lower eukayotes often do nothave UDP specific diphosphatase activity in the Golgi since they do notutilize UDP-sugar precursors for glycoprotein synthesis in the Golgi.Schizosaccharomyces pombe, a yeast found to add galactose residues tocell wall polysaccharides (from UDP-galactose) was found to havespecific UDPase activity further suggesting the requirement for such anenzyme (Berninsone, 1994). UDP is known to be a potent inhibitor ofglycosyltransferases and the removal of this glycosylation side productis important in order to prevent glycosyltransferase inhibition in thelumen of the Golgi (Khatara et al. 1974).

Expression of GnTs to Produce Complex N-glycans

Expression of GnT-III to Boost Antibody Functionality

The addition of an N-acetylglucosamine to the GlcNAc₁Man₃GlcNAc₂structure by N-acetylglucosaminyltransferases II and III yields aso-called bisected N-glycan GlcNAc₃Man₃GlcNAc₂ (FIG. 3). This structurehas been implicated in greater antibody-dependent cellular cytotoxicity(ADCC) (Umana et al. 1999). Re-engineering glycoforms of immunoglobulinsexpressed by mammalian cells is a tedious and cumbersome task.Especially in the case of GnTIII, where over-expression of this enzymehas been implicated in growth inhibition, methods involving regulated(inducible) gene expression had to be employed to produceimmunoglobulins with bisected N-glycans (Umana et al 1999a, 1999b).

Accordingly, in another embodiment, the invention provides systems andmethods for producing human-like N-glycans having bisectingN-acetylglucosamine (GlcNAcs) on the core mannose structure. In apreferred embodiment, the invention provides a system and method forproducing immunoglobulins having bisected N-glycans. The systems andmethods described herein will not suffer from previous problems, e.g.,cytotoxicity associated with overexpression of GnTIII or ADCC, as thehost cells of the invention are engineered and selected to be viable andpreferably robust cells which produce N-glycans having substantiallymodified human-type glycoforms such as GlcNAc₂Man₃GlcNAc₂. Thus,addition of a bisecting N-acetylglucosamine in a host cell of theinvention will have a negligible effect on the growth-phenotype orviability of those host cells.

In addition, previous work (Umana) has shown that there is no linearcorrelation between GnTIII expression levels and the degree of ADCC.Finding the optimal expression level in mammalian cells and maintainingit throughout an FDA approved fermentation process seems to be achallenge. However, in cells of the invention, such as fungal cells,finding a promoter of appropriate strength to establish a robust,reliable and optimal GnTIII expression level is a comparatively easytask for one of skill in the art.

A host cell such as a yeast strain capable of producing glycoproteinswith bisecting N-glycans is engineered according to the invention, byintroducing into the host cell a GnTIII activity (Example 6).Preferably, the host cell is transformed with a nucleic acid thatencodes GnTIII (see, e.g., FIG. 32) or a domain thereof having enzymaticactivity, optionally fused to a heterologous cell signal targetingpeptide (e.g., using the libraries and associated methods of theinvention.) Host cells engineereded to express GnTIII will producehigher antibody titers than mammalian cells are capable of. They willalso produce antibodies with higher potency with respect to ADCC.

Antibodies produced by mammalian cell lines transfected with GnTIII havebeen shown to be as effective as antibodies produced by non-transfectedcell-lines, but at a 10-20 fold lower concentration (Davies et al.2001). An increase of productivity of the production vehicle of theinvention over mammalian systems by a factor of twenty, and a ten-foldincrease of potency will result in a net-productivity improvement of twohundred. The invention thus provides a system and method for producinghigh titers of an antibody having high potency (e.g., up to severalorders of magnitude more potent than what can currently be produced).The system and method is safe and provides high potency antibodies atlow cost in short periods of time. Host cells engineered to express GnTIII according to the invention produce immunoglobulins having bisectedN-glycans at rates of at least 50 mg/liter/day to at least 500mg/liter/day. In addition, each immunoglobulin (Ig) molecule (comprisingbisecting GlcNAcs) is more potent than the same Ig molecule producedwithout bisecting GlcNAcs.

Cloning and Expression of GnT-IV and GnT-V

All branching structures in complex N-glycans are synthesized on acommon core-pentasaccharide (Man₃GlcNAc₂ or Man alpha1-6(Manalpha1-3)Man beta1-4 GlcNAc beta1-4 GlcNAc beta1-4 or Man₃GlcNAc₂) byN-acetylglucosamine transferases (GnTs) -I to -VI (Schachter H et al.(1989) Methods Enzymo; 179:351-97). Current understanding of thebiosynthesis of more highly branched N-glycans suggests that after theaction of GnTII (generation of GlcNAc₂Man₃GlcNAc₂ structures) GnTIVtransfers GlcNAc from UDP-GlcNAc in beta1,4 linkage to the Man alpha1,3Man beta1,4 arm of GlcNAc₂Man₃GlcNAc₂ N-glycans (Allen S D et al. (1984)J Biol Chem. June 10; 259(11):6984-90; and Gleeson P A and Schachter H.J (1983); J. Biol Chem 25; 258(10):6162-73) resulting in a triantennaryagalacto sugar chain. This N-glycan (GlcNAc beta1-2 Man alpha1-6(GlcNAcbeta1-2 Man alpha1-3) Man beta1-4 GlcNAc beta 1-4 GlcNAc beta1,4 Asn) isa common substrate for GnT-III and -V, leading to the synthesis ofbisected, tri- and tetra-antennary structures. Where the action ofGnTIII results in a bisected N-glycan and where GnTV catalyzes theaddition of beta 1-6GlcNAc to the alpha 1-6 mannosyl core, creating thebeta 1-6 branch. Addition of galactose and sialic acid to these branchesleads to the generation of a fully sialylated complex N-glycan.

Branched complex N-glycans have been implicated in the physiologicalactivity of therapeutic proteins, such as human erythropoietin (hEPO).Human EPO having bi-antennary structures has been shown to have a lowactivity, whereas hEPO having tetra-antennary structures resulted inslower clearance from the bloodstream and thus in higher activity(Misaizu T et al. (1995) Blood December 1; 86(11):4097-104).

With DNA sequence information, the skilled worker can clone DNAmolecules encoding GnT IV and/or V activities (Example 6; FIGS. 33 and34). Using standard techniques well-known to those of skill in the art,nucleic acid molecules encoding GnT IV or V (or encoding catalyticallyactive fragments thereof) may be inserted into appropriate expressionvectors under the transcriptional control of promoters and otherexpression control sequences capable of driving transcription in aselected host cell of the invention, e.g., a fungal host such as Pichiasp., Kluyveromyces sp. and Aspergillus sp., as described herein, suchthat one or more of these mammalian GnT enzymes may be activelyexpressed in a host cell of choice for production of a human-likecomplex glycoprotein.

The following are examples which illustrate the compositions and methodsof this invention. These examples should not be construed as limiting:the examples are included for the purposes of illustration only.

EXAMPLE 1 Identification, Cloning and Deletion of the ALG3 Gene in P.pastoris and K. lactis

Degenerate primers were generated based on an alignment of Alg3 proteinsequences from S. cerevisiae, H. sapiens, and D. melanogaster and wereused to amplify an 83 bp product from P. pastoris genomic DNA:5′-GGTGTTTTGTTTTCTAGATCTTTGCAYTAYCARTT-3′ (SEQ ID NO. 1) and5′-AGAATTTGGTGGGTAAGAATTCCA-RCACCAYTCRTG-3′ (SEQ ID NO. 2). Theresulting PCR product was cloned into the pCR2.1 vector (Invitrogen,Carlsbad, Calif.) and sequence analysis revealed homology to knownALG3/RHK1/NOT56 homologs (Genbank NC.sub.—001134.2, AF309689,NC.sub.—003424.1). Subsequently, 1929 bp upstream and 2738 bp downstreamof the initial PCR product were amplified from a P. pastoris genomic DNAlibrary (Boehm, T. Yeast May 1999; 15(7):563-72) using the internaloligonucleotides 5′-CCTAAGCTGGTATGCGTTCTCTTTGCCATATC-3′ (SEQ ID NO. 3)and 5′-GCGGCATAAACAATAATAGATGCTATAAAG-3′ (SEQ ID NO. 4) along with T3(5′-AATTAACCCTCACTAAAGGG-3′) (SEQ ID NO. 5) and T7 (5′-GTAATACGACTCACTATAGGGC-3′) (SEQ ID NO. 6) (Integrated DNA Technologies,Coralville, Iowa) in the backbone of the library bearing plasmid lambdaZAP II (Stratagene, La Jolla, Calif.). The resulting fragments werecloned into the pCR2.1-TOPO vector (Invitrogen) and sequenced. From thissequence, a 1395 bp ORF was identified that encodes a protein with 35%identity and 53% similarity to the S. cerevisiae ALG3 gene (using BLASTprograms). The gene was named PpALG3.

The sequence of PpALG3 was used to create a set of primers to generate adeletion construct of the PpALG3 gene by PCR overlap (Davidson et al,2002 Microbiol. 148(Pt 8):2607-15). Primers below were used to amplify 1kb regions 5′ and 3′ of the PpALG3 ORF and the KAN^(R) gene,respectively:

RCD142 (SEQ ID NO. 7) (5′-CCACATCATCCGTGCTACATATAG-3′), RCD144(SEQ ID NO. 8) (5′-ACGAGGCAAGCTAAACAGATCTCGAAGTATCGAGGG TTATCCAG-3′),RCD145 (SEQ ID NO. 9) (5′-CCATCCAGTGTCGAAAACGAGCCAATGGTTCATGTCTATAAATC-3′), RCD147 (SEQ ID NO. 10) (5′-AGCCTCAGCGCCAACAAGCGATGG-3′),RCD143 (SEQ ID NO. 11) (5′-CTGGATAACCCTCGATACTTCGAGATCTGTTTAGCTTGCCTCGT-3′), and RCD146 (SEQ ID NO. 12)(5′-GATTTATAGACATGAACCATTGGCTCGTTTTCGACA CTGGATGG-3′).Subsequently, primers RCD142 and RCD147 were used to overlap the threeresulting PCR products into a single 3.6 kb alg3::KAN^(R) deletionallele.Identification, Cloning and Deletion of the ALG3 Gene in K. lactis.

The ALG3p sequences from S. cerevisiae, Drosophila melanogaster, Homosapiens etc were aligned with K. lactis sequences (PENDANT ESTdatabase). Regions of high homology that were in common homologs butdistinct in exact sequence from the homologs were used to create pairsof degenerate primers that were directed against genomic DNA from the K.lactis strain MG 1/2 (Bianchi et al, 1987). In the case of ALG3, PCRamplification with primers KAL-1 (5′-ATCCTTTACCGATGCTGTAT-3′) (SEQ IDNO. 13) and KAL-2 (5′-ATAACAGTATGTGTTACACGCGTGTAG-3′) (SEQ ID NO. 14)resulted in a product that was cloned and sequenced and the predictedtranslation was shown to have a high degree of homology to Alg3pproteins (>50% to S. cerevisiae Alg3p).

The PCR product was used to probe a Southern blot of genomic DNA from K.lactis strain (MG1/2) with high stringency (Sambrook et al, 1989).Hybridization was observed in a pattern consistent with a single gene.This Southern blot was used to map the genomic loci. Genomic fragmentswere cloned by digesting genomic DNA and ligating those fragments in theappropriate size-range into pUC19 to create a K. lactis subgenomiclibrary. This subgenomic library was transformed into E. coli andseveral hundred clones were tested by colony PCR, using primers KAL-1and KAL-2. The clones containing the predicted KlALG3 and KlALG61 geneswere sequenced and open reading frames identified.

Primers for construction of an alg3::NAT^(R) deletion allele, using aPCR overlap method (Davidson et al, 2002), were designed and theresulting deletion allele was transformed into two K. lactis strains andNAT-resistant colonies selected. These colonies were screened by PCR andtransformants were obtained in which the ALG3 ORF was replaced with theoch1::NAT^(R) mutant allele.

EXAMPLE 2 Generation of an alg3/och1 Mutant Strain Expressing anα-1,2-Mannosidase, GnT1 and GnTII for Production of a Human-LikeGlycoprotein

The 1215 bp open reading frame of the P. pastoris OCH1 gene as well as2685 bp upstream and 1175 bp downstream was amplified by PCR (B. K. Choiet al., submitted to Proc. Natl. Acad. Sci. USA 2002; see also WO02/00879; each of which is incorporated herein by reference), clonedinto the pCR2.1-TOPO vector (Invitrogen) and designated pBK9. To createan och1 knockout strain containing multiple auxotrophic markers, 100 μgof pJN329, a plasmid containing an och1::URA3 mutant allele flanked withSfiI restriction sites was digested with SfiI and used to transform P.pastoris strain JC308 (Cereghino et al. Gene 263 (2001) 159-169) byelectroporation. Following incubation on defined medium lacking uracilfor 10 days at room temperature, 1000 colonies were picked andre-streaked. URA⁺ clones that were unable to grow at 37° C., but grew atroom temperature, were subjected to colony PCR to test for the correctintegration of the och1::URA3 mutant allele. One clone that exhibitedthe expected PCR pattern was designated YJN153. The Kringle 3 domain ofhuman plasminogen (K3) was used as a model protein. A Neo^(R) markedplasmid containing the K3 gene was transformed into strain YJN153 and aresulting strain, expressing K3, was named BK64-1 (B. K. Choi et al,submitted to Proc. Natl. Acad. Sci. USA 2002).

Plasmid pPB103, containing the Kluyveromyces lactis MNN2-2 gene,encoding a Golgi UDP-N-acetylglucosamine transporter was constructed bycloning a blunt BglII-HindIII fragment from vector pDL02 (Abeijon et al.(1996) Proc. Natl. Acad. Sci. U.S.A. 93:5963-5968) into BglII and BamHIdigested and blunt ended pBLADE-SX containing the P. pastoris ADE1 gene(Cereghino et al. (2001) Gene 263:159-169). This plasmid was linearizedwith EcoNI and transformed into strain BK64-1 by electroporation and onestrain confirmed to contain the MNN2-2 by PCR analysis was named PBP1.

A library of mannosidase constructs was generated, comprising in-framefusions of the leader domains of several type I or type II membraneproteins from S. cerevisiae and P. pastoris fused with the catalyticdomains of several α-1,2-mannosidase genes from human, mouse, fly, wormand yeast sources (see, e.g., WO02/00879, incorporated herein byreference). This library was created in a P. pastoris HIS4 integrationvector and screened by linearizing with SalI, transforming byelectroporation into strain PBP1, and analyzing the glycans releasedfrom the K3 reporter protein. One active construct chosen was a chimeraof the 988-1296 nucleotides (C-terminus) of the yeast SEC12 gene fusedwith a N-terminal deletion of the mouse α-1,2-mannosidase IA (MmMannIA)gene, which was missing the 187 nucleotides. A P. pastoris strainexpressing this construct was named PBP2.

A library of GnTI constructs was generated, comprising in-frame fusionsof the same leader library with the catalytic domains of GnTI genes fromhuman, worm, frog and fly sources (WO 02/00879). This library wascreated in a P. pastoris ARG4 integration vector and screened bylinearizing with AatII, transforming by electroporation into strainPBP2, and analyzing the glycans released from K3. One active constructchosen was a chimera of the first 120 bp of the S. cerevisiae MNN9 genefused to a deletion of the human GnTI gene, which was missing the first154 bp. A P. pastoris strain expressing this construct was named PBP3.

Subsequently, a P. pastoris alg3::KAN^(R) deletion construct wasgenerated as described above. Approximately 5 μg of the resulting PCRproduct was transformed into strain PBP3 and colonies were selected onYPD medium containing 200 μg/ml G418. One strain out of 20 screened byPCR was confirmed to contain the correct integration of thealg3::KAN^(R) mutant allele and lack the wild-type allele. This strainwas named RDP27.

Finally, a library of GnTII constructs was generated, which wascomprised of in-frame fusions of the leader library with the catalyticdomains of GnTII genes from human and rat sources (WO 02/00879). Thislibrary was created in a P. pastoris integration vector containing theNST^(R) gene conferring resistance to the drug nourseothricin. Thelibrary plasmids were linearized with EcoRI, transformed into strainRDP27 by electroporation, and the resulting strains were screened byanalysis of the released glycans from purified K3.

Materials

MOPS, sodium cacodylate, manganese chloride, UDP-galactose andCMP-N-acetylneuraminic acid were from SIGMA®. TFA was from ALDRICH®.Recombinant rat a2,6-sialyltransferase from Spodoptera frugiperda andbeta 1,4-galactosyltransferase from bovine milk were from CALBIOCHEM®.Protein N-glycosidase F, mannosidases, and oligosaccharides were fromGLYKO® (San Rafael, Calif.). DEAE TOYOPEARL® resin was from TosoHaas.Metal chelating “HisBind” resin was from Novagen (Madison, Wis.).96-well lysate-clearing plates were from Promega (Madison, Wis.).Protein-binding 96-well plates were from Millipore (Bedford, Mass.).Salts and buffering agents were from SIGMA® (St. Louis, Mo.). MALDImatrices were from ALDRICH® (Milwaukee, Wis.).

Protein Purification

Kringle 3 was purified using a 96-well format on a Beckman BioMek 2000sample-handling robot (Beckman/Coulter Ranch Cucamonga, Calif.). Kringle3 was purified from expression media using a C-terminal hexa-histidinetag. The robotic purification is an adaptation of the protocol providedby Novagen for their HisBind resin. Briefly, a 150 uL (μL) settledvolume of resin is poured into the wells of a 96-well lysate-bindingplate, washed with 3 volumes of water and charged with 5 volumes of 50mM NiSO4 and washed with 3 volumes of binding buffer (5 mM imidazole,0.5M NaCl, 20 mM Tris-HCL pH7.9). The protein expression media isdiluted 3:2, media/PBS (60 mM PO4, 16 mM KCl, 822 mM NaCl pH7.4) andloaded onto the columns. After draining, the columns are washed with 10volumes of binding buffer and 6 volumes of wash buffer (30 mM imidazole,0.5M NaCl, 20 mM Tris-HCl pH7.9) and the protein is eluted with 6volumes of elution buffer (1M imidazole, 0.5M NaCl, 20 mM Tris-HClpH7.9). The eluted glycoproteins are evaporated to dryness bylyophilyzation.

Release of N-Linked Glycans

The glycans are released and separated from the glycoproteins by amodification of a previously reported method (Papac, et al. A. J. S.(1998) Glycobiology 8, 445-454). The wells of a 96-well Multi Screen IP(Immobilon-P membrane) plate (Millipore) are wetted with 100 uL ofmethanol, washed with 3×150 uL of water and 50 uL of RCM buffer (8Murea, 360 mM Tris, 3.2 mM EDTA pH8.6), draining with gentle vacuum aftereach addition. The dried protein samples are dissolved in 30 uL of RCMbuffer and transferred to the wells containing 10 uL of RCM buffer. Thewells are drained and washed twice with RCM buffer. The proteins arereduced by addition of 60 uL of 0.1M DTT in RCM buffer for 1 hr at 37°C. The wells are washed three times with 300 uL of water andcarboxymethylated by addition of 60 uL of 0.1M iodoacetic acid for 30min in the dark at room temperature. The wells are again washed threetimes with water and the membranes blocked by the addition of 100 uL of1% PVP 360 in water for 1 hr at room temperature. The wells are drainedand washed three times with 300 uL of water and deglycosylated by theaddition of 30 uL of 10 mM NH4HCO3 pH 8.3 containing one milliunit ofN-glycanase (Glyko). After 16 hours at 37° C., the solution containingthe glycans was removed by centrifugation and evaporated to dryness.

Matrix Assisted Laser Desorption Ionization Time of Flight MassSpectrometry

Molecular weights of the glycans were determined using a Voyager DE PROlinear MALDI-TOF (Applied Biosciences) mass spectrometer using delayedextraction. The dried glycans from each well were dissolved in 15 uL ofwater and 0.5 uL spotted on stainless steel sample plates and mixed with0.5 uL of S-DHB matrix (9 mg/mL of dihydroxybehzoic acid, 1 mg/mL of5-methoxysalicilic acid in 1:1 water/acetonitrile 0.1% TFA) and allowedto dry.

Ions were generated by irradiation with a pulsed nitrogen laser (337 nm)with a 4 ns pulse time. The instrument was operated in the delayedextraction mode with a 125 ns delay and an accelerating voltage of 20kV. The grid voltage was 93.00%, guide wire voltage was 0.10%, theinternal pressure was less than 5×10-7 torr, and the low mass gate was875 Da. Spectra were generated from the sum of 100-200 laser pulses andacquired with a 2 GHz digitizer. Man5 oligosaccharide was used as anexternal molecular weight standard. All spectra were generated with theinstrument in the positive ion mode. The estimated mass accuracy of thespectra was 0.5%.

Materials:

MOPS, sodium cacodylate, manganese chloride, UDP-galactose andCMP-N-acetylneuraminic acid were from SIGMA®, Saint Louis, Mo.Trifluroacetic acid (TFA) was from SIGMA/ALDRICH®., Saint Louis, Mo.Recombinant rat alpha-2,6-sialyltransferase from Spodoptera frugiperdaand beta-1,4-galactosyltransferase from bovine milk were fromCALBIOCHEM®, San Diego, Calif.

β-N-acetylhexosaminidase Digestion

The glycans were released and separated from the glycoproteins by amodification of a previously reported method (Papac, et al. A. J. S.(1998) Glycobiology 8, 445-454). After the proteins were reduced andcarboxymethylated, and the membranes blocked, the wells were washedthree time with water. The protein was deglycosylated by the addition of30 μl of 10 mM NH₄HCO₃ pH 8.3 containing one milliunit of N-glycanase(Glyko, Novato, Calif.). After 16 hr at 37° C., the solution containingthe glycans was removed by centrifugation and evaporated to dryness. Theglycans were then dried in SC210A speed vac (Thermo Savant, Halbrook,N.Y.). The dried glycans were put in 50 mM NH₄Ac pH 5.0 at 37° C.overnight and 1 mU of hexos (Glyko, Novato, Calif.) was added.

Galactosyltransferase Reaction

Approximately 2 mg of protein (r-K3:hPg [PBP6-5]) was purified bynickel-affinity chromatography, extensively dialyzed against 0.1% TFA,and lyophilized to dryness. The protein was redissolved in 150 μL of 50mM MOPS, 20 mM MnCl2, pH7.4. After addition of 32.5 μg (533 nmol) ofUDP-galactose and 4 mU of β 1,4-galactosyltransferase, the sample wasincubated at 37° C. for 18 hours. The samples were then dialyzed against0.1% TFA for analysis by MALDI-TOF mass spectrometry.

The spectrum of the protein reacted with galactosyltransferase showed anincrease in mass consistent with the addition of two galactose moietieswhen compared with the spectrum of a similar protein sample incubatedwithout enzyme. Protein samples were next reduced, carboxymethylated anddeglycosylated with PNGase F. The recovered N-glycans were analyzed byMALDI-TOF mass spectrometry. The mass of the predominant glycan from thegalactosyltransferase reacted protein was greater than that of thecontrol glycan by a mass consistent with the addition of two galactosemoieties (325.4 Da).

Sialyltransferase Reaction

After resuspending the (galactosyltransferase reacted) proteins in 10 μLof 50 mM sodium cacodylate buffer pH6.0, 300 μg (488 nmol) ofCMP-N-acetylneuraminic acid (CMP-NANA) dissolved in 15 μL of the samebuffer, and 5 μL (2 mU) of recombinant α-2,6 sialyltransferase wereadded. After incubation at 37° C. for 15 hours, an additional 200 μg ofCMP-NANA and 1 mU of sialyltransferase were added. The protein sampleswere incubated for an additional 8 hours and then dialyzed and analyzedby MALDI-TOF-MS as above.

The spectrum of the glycoprotein reacted with sialyltransferase showedan increase in mass when compared with that of the starting material(the protein after galactosyltransferase reaction). The N-glycans werereleased and analyzed as above. The increase in mass of the twoion-adducts of the predominant glycan was consistent with the additionof two sialic acid residues (580 and 583 Da).

EXAMPLE 3 Identification, Cloning and Deletion of the ALG9 and ALG 12Genes in P. pastoris

Similar to Example 1, the ALG9p and ALG12 sequences, respectively fromS. cerevisiae, Drosophila melanogaster, Homo sapiens, etc., is alignedand regions of high homology are used to design degenerate primers.These primers are employed in a PCR reaction on genomic DNA from the P.pastoris. The resulting initial PCR product is subcloned, sequenced andused to probe a Southern blot of genomic DNA from P. pastoris with highstringency (Sambrook et al., 1989). Hybridization is observed. ThisSouthern blot is used to map the genomic loci. Genomic fragments arecloned by digesting genomic DNA and ligating those fragments in theappropriate size-range into pUC19 to create a P. pastoris subgenomiclibrary. This subgenomic library is transformed into E. coli and severalhundred clones tested by colony PCR, using primers designed based on thesequence of the initial PCR product. The clones containing the predictedgenes are sequenced and open reading frames identified. Primers forconstruction of an alg9::NAT^(R) deletion allele, using a PCR overlapmethod (Davidson et al., 2002), are designed. The resulting deletionallele is transformed into two P. pastoris strains and NAT resistantcolonies are selected. These colonies are screened by PCR andtransformants obtained in which the ALG9 ORF is replaced with theoch1::NAT^(R) mutant allele. See generally, Cipollo et al. Glycobiology2002 (12)11:749-762; Chantret et al. J. Biol. Chem. Jul. 12, 2002(277)28:25815-25822; Cipollo et al. J. Biol. Chem. Feb. 11, 2000(275)6:4267-4277; Burda et al. Proc. Natl. Acad. Sci. U.S.A. July 1996(93):7160-7165; Karaoglu et al. Biochemistry 2001, 40, 12193-12206;Grimme et al. J. Biol. Chem. Jul. 20, 2001 (276)29:27731-27739; Verosteket al. J. Biol. Chem. Jun. 5, 1993 (268)16:12095-12103; Huffaker et al.Proc. Natl. Acad. Sci. U.S.A. December 1983 (80):7466-7470.

EXAMPLE 4 Identification, Cloning and Expression of Alpha 1,2-3Mannosidase from Xanthomonas Manihotis

The alpha 1,2-3 Mannosidase from Xanthomonas Manihotis has twoactivities: an alpha-1,2 and an alpha-1,3 mannosidase. The methods ofthe invention may also use two independent mannosidases having theseactivities, which may be similarly identified and cloned from a selectedorganism of interest.

As described by Landry et al., alpha-mannosidases can be purified fromXanthomonas sp., such as Xanthomonas manihotis. X. manihotis can bepurchased from the American Type Culture Collection (ATCC catalog number49764) (Xanthomonas axonopodis Starr and Garces pathovar manihotisdeposited as Xanthomonas manihotis (Arthaud-Berthet) Starr). Enzymes arepurified from crude cell-extracts as previously described (Wong-Madden,S. T. and Landry, D. (1995) Purification and characterization of novelglycosidases from the bacterial genus Xanthomonas; and Landry, D. U.S.Pat. No. 6,300,113 B1 Isolation and composition of novel Glycosidases).After purification of the mannosidase, one of several methods are usedto obtain peptide sequence tags (see, e.g., W. Quadroni M et al. (2000).A method for the chemical generation of N-terminal peptide sequence tagsfor rapid protein identification. Anal Chem (2000) March 1;72(5):1006-14; Wilkins M R et al. Rapid protein identification usingN-terminal “sequence tag” and amino acid analysis. Biochem Biophys ResCommun. (1996) April 25; 221(3):609-13; and Tsugita A. (1987)Developments in protein microsequencing. Adv Biophys (1987) 23:81-113).

Sequence tags generated using a method above are then used to generatesets of degenerate primers using methods well-known to the skilledworker. Degenerate primers are used to prime DNA amplification inpolymerase chain reactions (e.g., using Taq polymerase kits according tomanufacturers' instructions) to amplify DNA fragments. The amplified DNAfragments are used as probes to isolate DNA molecules comprising thegene encoding a desired mannosidase, e.g., using standard Southern DNAhybridization techniques to identify and isolate (clone) genomic piecesencoding the enzyme of interest. The genomic DNA molecules are sequencedand putative open reading frames and coding sequences are identified. Asuitable expression construct encoding for the glycosidase of interestcan then be generated using methods described herein and well-known inthe art.

Nucleic acid fragments comprising sequences encoding alpha 1,2-3mannosidase activity (or catalytically active fragments thereof) arecloned into appropriate expression vectors for expression, andpreferably targeted expression, of these activities in an appropriatehost cell according to the methods set forth herein.

EXAMPLE 5 Identification, Cloning and Expression of the ALG6 Gene in P.pastoris

Similar to Example 1, the ALG6p sequences from S. cerevisiae, Drosophilamelanogaster, Homo sapiens etc., are aligned and regions of highhomology are used to design degenerate primers. These primers areemployed in a PCR reaction on genomic DNA from the P. pastoris. Theresulting initial PCR product is subcloned, sequenced and used to probea Southern blot of genomic DNA from P. pastoris with high stringency(Sambrook et al, 1989). Hybridization is observed. This Southern blot isused to map the genomic loci. Genomic fragments are cloned by digestinggenomic DNA and ligating those fragments in the appropriate size-rangeinto pUC19 to create a P. pastoris subgenomic library. This subgenomiclibrary is transformed into E. coli and several hundred clones aretested by colony PCR, using primers designed based on the sequence ofthe initial PCR product. The clones containing the predicted genes aresequenced and open reading frames identified. Primers for constructionof an alg6::NAT^(R) deletion allele, using a PCR overlap method(Davidson et al, 2002), are designed and the resulting deletion alleleis transformed into two P. pastoris strains and NAT resistant coloniesselected. These colonies are screened by PCR and transformants areobtained in which the ALG6 ORF is replaced with the och1::NAT^(R) mutantallele. See, e.g., Imbach et al. Proc. Natl. Acad. Sci. U.S.A. June 1999(96)6982-6987.

Nucleic acid fragments comprising sequences encoding Alg6p (orcatalytically active fragments thereof) are cloned into appropriateexpression vectors for expression, and preferably targeted expression,of these activities in an appropriate host cell according to the methodsset forth herein. The cloned ALG6 gene can be brought under the controlof any suitable promoter to achieve overexpression. Even expression ofthe gene under the control of its own promoter is possible. Expressionfrom multicopy plasmids will generate high levels of expression(“overexpression”).

EXAMPLE 6 Cloning and Expression of GnT III to Produce Bisecting GlcNAcswhich Boost Antibody Functionality

A. Background

The addition of an N-acetylglucosamine to the GlcNAc₂Man₃GlcNAc₂structure by N-acetylglucosaminyltransferases III yields a so-calledbisected N-glycan (see FIG. 3). This structure has been implicated ingreater antibody-dependent cellular cytotoxicity (ADCC) (Umana et al.1999).

A host cell such as a yeast strain capable of producing glycoproteinswith bisected N-glycans is engineered according to the invention, byintroducing into the host cell a GnTIII activity. Preferably, the hostcell is transformed with a nucleic acid that encodes GnTIII (e.g., amammalian such as the murine GnT III shown in FIG. 32) or a domainthereof having enzymatic activity, optionally fused to a heterologouscell signal targeting peptide (e.g., using the libraries and associatedmethods of the invention.)

IgGs consist of two heavy-chains (V_(H), C_(H)1, C_(H)2 and C_(H)3 inFIG. 30), interconnected in the hinge region through three disulfidebridges, and two light chains (V_(L), C_(L) in FIG. 30). The lightchains (domains V_(L) and C_(L)) are linked by another disulfide bridgeto the C_(H)1 portion of the heavy chain and together with the C_(H)1and V_(H) fragment make up the so-called Fab region. Antigens bind tothe terminal portion of the Fab region. The Fc region of IgGs consistsof the C_(H)3, the C_(H) ² and the hinge region and is responsible forthe exertion of so-called effector functions (see below).

The primary function of antibodies is binding to an antigen. However,unless binding to the antigen directly inactivates the antigen (such asin the case of bacterial toxins), mere binding is meaningless unlessso-called effector-functions are triggered. Antibodies of the IgGsubclass exert two major effector-functions: the activation of thecomplement system and induction of phagocytosis. The complement systemconsists of a complex group of serum proteins involved in controllinginflammatory events, in the activation of phagocytes and in the lyticaldestruction of cell membranes. Complement activation starts with bindingof the C1 complex to the Fc portion of two IgGs in close proximity. C1consists of one molecule, C1q, and two molecules, C1r and C1s.Phagocytosis is initiated through an interaction between the IgG's Fcfragment and Fc-gamma-receptors (FcγRI, II and III in FIG. 30). Fcreceptors are primarily expressed on the surface of effector cells ofthe immune system, in particular macrophages, monocytes, myeloid cellsand dendritic cells.

The C_(H)2 portion harbors a conserved N-glycosylation site atasparagine 297 (Asp297). The Asp297 N-glycans are highly heterogeneousand are known to affect Fc receptor binding and complement activation.Only a minority (i.e., about 15-20%) of IgGs bears a disialylated, and3-10% have a monosialylated N-glycan (reviewed in Jefferis, R.,Glycosylation of human IgG Antibodies. BioPharm, 2001). Interestingly,the minimal N-glycan structure shown to be necessary for fullyfunctional antibodies capable of complement activation and Fc receptorbinding is a pentasacharide with terminal N-acetylglucosamine residues(GlcNAc.sub.2Man.sub.3) (reviewed in Jefferis, R., Glycosylation ofhuman IgG Antibodies. BioPharm, 2001). Antibodies with less than aGlcNAc.sub.2Man.sub.3 N-glycan or no N-glycosylation at Asp297 mightstill be able to bind an antigen but most likely will not activate thecrucial downstream events such as phagocytosis and complementactivation. In addition, antibodies with fungal-type N-glycans attachedto Asp297 will in all likelihood solicit an immune-response in amammalian organism which will render that antibody useless as atherapeutic glycoprotein.

B. Cloning and Expression of GnTIII

The DNA fragment encoding part of the mouse GnTIII protein lacking theTM domain is PCR amplified from murine (or other mammalian) genomic DNAusing forward 5′-TCCTGGCGCGCCTTCCCGAGAGAACTGGCCTCCCTC-3′ (SEQ ID NO. 15)and 5′-AATTAATTAACCCTAGCCCTCCGCTGTATCCAACTTG-3′ (SEQ ID NO. 16) reversedprimers. Those primers include AscI and PacI restriction sites that willbe used for cloning into the vector suitable for the fusion with leaderlibrary. The nucleic acid and amino acid sequence of murine GnTIII isshown in FIG. 32.

C. Cloning of Immunoglobulin Encoding Sequences

Protocols for the cloning of the variable regions of antibodies,including primer sequences, have been published previously. Sources ofantibodies and encoding genes can be, among others, in vitro immunizedhuman B cells (see, e.g., Borreback, C. A. et al. (1988) Proc. Natl.Acad. Sci. USA 85, 3995-3999), periphal blood lymphocytes or singlehuman B cells (see, e.g., Lagerkvist, A. C. et al. (1995) Biotechniques18, 862-869; and Terness, P. et al. (1997) Hum. Immunol. 56, 17-27) andtransgenic mice containing human immunoglobulin loci, allowing thecreation of hybridoma cell-lines.

Using standard recombinant DNA techniques, antibody-encoding nucleicacid sequences can be cloned. Sources for the genetic informationencoding immunoglobulins of interest are typically total RNApreparations from cells of interest, such as blood lymphocytes orhybridoma cell lines. For example, by employing a PCR based protocolwith specific primers, variable regions can be cloned via reversetranscription initiated from a sequence-specific primer hybridizing tothe IgG C_(H)1 domain site and a second primer encoding amino acids111-118 of the murine kappa constant region. The V_(H) and V_(K)encodingcDNAs will then be amplified as previously published (see, e.g.,Graziano, R. F. et al. (1995) J Immunol. 155(10): p. 4996-5002;Welschof, M. et al. (1995) J. Immunol. Methods 179, 203-214; andOrlandi, R. et al. (1988) Proc. Natl. Acad. Sci. USA 86: 3833). Cloningprocedures for whole immunoglobulins (heavy and light chains have alsobeen published (see, e.g., Buckel, P. et al. (1987) Gene 51:13-19;Recinos A 3^(rd) et al. (1994) Gene 149:385-386; (1995) Gene June 9;158(2):311-2; and Recinos A 3^(rd) et al. (1994) Gene November 18;149(2):385-6). Additional protocols for the cloning and generation ofantibody fragment and antibody expression constructs have been describedin Antibody Engineering, R. Kontermann and S. Dübel (2001), Editors,Springer Verlag: Berlin Heidelberg N.Y.

Fungal expression plasmids encoding heavy and light chain ofimmunoglobulins have been described (see, e.g., Abdel-Salam, H. A. etal. (2001) Appl. Microbiol. Biotechnol. 56: 157-164; and Ogunjimi, A. A.et al. (1999) Biotechnology Letters 21: 561-567). One can thus generateexpression plasmids harboring the constant regions of immunoglobulins.To facilitate the cloning of variable regions into these expressionvectors, suitable restriction sites can be placed in close proximity tothe termini of the variable regions. The constant regions can beconstructed in such a way that the variable regions can be easilyin-frame fused to them by a simple restriction-digest/ligationexperiment. FIG. 31 shows a schematic overview of such an expressionconstruct, designed in a very modular way, allowing easy exchange ofpromoters, transcriptional terminators, integration targeting domainsand even selection markers.

As shown in FIG. 31, V_(L) as well as V_(H) domains of choice can beeasily cloned in-frame with C_(L) and the C_(H) regions, respectively.Initial integration is targeted to the P. pastoris AOX locus (orhomologous locus in another fungal cell) and the methanol-inducible AOXpromoter will drive expression. Alternatively, any other desiredconstitutive or inducible promoter cassette may be used. Thus, ifdesired, the 5′AOX and 3′AOX regions as well as transcriptionalterminator (TT) fragments can be easily replaced with different TT,promoter and integration targeting domains to optimize expression.Initially the alpha-factor secretion signal with the standard KEXprotease site is employed to facilitate secretion of heavy and lightchains. The properties of the expression vector may be further refinedusing standard techniques.

An Ig expression vector such as the one described above is introducedinto a host cell of the invention that expresses GnTIII, preferably inthe Golgi apparatus of the host cell. The Ig molecules expressed in sucha host cell comprise N-glycans having bisecting GlcNAcs.

EXAMPLE 7 Cloning and Expression of GnT-IV (UDP-GlcNAc:alpha-1,3-D-mannoside beta-1,4-N-Acetylglucosaminyltransferase IV) and GnT-V (beta1-6-N-acetylglucosaminyltransferase)

GnTIV-encoding cDNAs were isolated from bovine and human cells (Minowa,M. T. et al. (1998) J. Biol. Chem. 273 (19), 11556-11562; and Yoshida,A. et al. (1999) Glycobiology 9 (3), 303-310. The DNA fragments encodingfull length and a part of the human GnT-IV protein (FIG. 33) lacking theTM domain are PCR amplified from the cDNA library using forward5′-AATGAGATGAGGCTCCGCAATGGAACTG-3′ (SEQ ID NO. 17),5′-CTGATTGCTTATCAACGAGAATTCCT-TG-3′ (SEQ ID NO. 18), and reverse5′-TGTTGGTTTCTCAGATGATCAGTTGGTG-3′ (SEQ ID NO. 19) primers,respectively. The resulting PCR products are cloned and sequenced.

Similarly, genes encoding GnT-V protein have been isolated from severalmammalian species, including mouse. (See, e.g., Alverez, K. et al.Glycobiology 12 (7),389-394 (2002)). The DNA fragments encoding fulllength and a part of the mouse GnT-V protein (FIG. 34) lacking the TMdomain are PCR amplified from the cDNA library using forward5′-AGAGAGAGATGGCTTTCTTTTCTCCCTGG-3′ (SEQ ID NO. 20),5′-AAATCAAGTGGATGAAGGACATGTGGC-3′ (SEQ ID NO. 21), and reverse5′-AGCGATGCTATAGGCAGTCTTTGCAGAG-3′ (SEQ ID NO. 22) primers,respectively. The resulting PCR products are cloned and sequenced.

Nucleic acid fragments comprising sequences encoding GnT IV or V (orcatalytically active fragments thereof) are cloned into appropriateexpression vectors for expression, and preferably targeted expression,of these activities in an appropriate host cell according to the methodsset forth herein.

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What is claimed is:
 1. A method for producing a recombinant glycoproteinin a Pichia pastoris host cell that lacks OCH1 activity, the methodcomprising the steps of diminishing or depleting the activity of one ormore enzymes-selected from the group consisting of: (a) an enzyme havingdolichyl-P-Man:Man₅GlcNAc₂-PP-dolichyl alpha-1,3 mannosyltransferaseactivity; (b) an enzyme having dolichyl-P-Man:Man₆GlcNAc₂-PP-dolichylalpha-1,2 mannosyltransferase activity; and (c) an enzyme havingdolichyl-P-Man:Man₇GlcNAc₂-PP-dolichyl alpha-1,6 mannosyltransferaseactivity, said host cell further expressing: (i) an α1,2-mannosidasecatalytic domain fused to a targeting peptide that targets theendoplasmic reticulum (ER) or Golgi apparatus in the host cell, (ii) aGlcNAc transferase I (GnT I) catalytic domain fused to a targetingpeptide that targets the ER or Golgi apparatus of the host cell, and(iii) the recombinant glycoprotein, wherein said method results in theproduction within the host cell of recombinant glycoproteins havingN-glycans attached thereto comprising GlcNAcMan_(x)GlcNAc₂ corestructures, wherein X is 3 or
 4. 2. The method of claim 1, wherein thehost cell further includes a nucleic acid molecule encoding amannosidase II catalytic domain fused to a targeting peptide thattargets the ER or Golgi apparatus of the host cell and the methodresults in the production within the host cell of recombinantglycoproteins having N-glycans attached thereto comprisingGlcNAcMan₃GlcNAc₂ core structures.
 3. The method of claim 2, wherein thehost cell further includes a nucleic acid molecule encoding a GnT IIcatalytic domain fused to a targeting peptide that targets the ER orGolgi apparatus of the host cell and the method results in theproduction within the host cell of recombinant glycoproteins havingN-glycans attached thereto comprising GlcNAc₂Man₃GlcNAc₂ corestructures.
 4. The method of claim 1 wherein the host cell furtherincludes a nucleic acid molecule encoding a GnT II catalytic domainfused to a targeting peptide that targets the ER or Golgi apparatus ofthe host cell and the method results in the production within the hostcell of recombinant glycoproteins having N-glycans attached theretocomprising GlcNAc₂Man₃GlcNAc₂ core structures.
 5. The method of claim 4,wherein the wherein the host cell further includes one or more nucleicacid molecules encoding one or more enzyme activities selected fromgalactosyltransferase, sialyltransferase, fucosyltransferase, and GlcNActransferase III, IV, V, and VI.
 6. The method of claim 1, wherein thediminished or depleted enzyme has dolichyl-P-Man:Man₅GlcNAc₂-PP-dolichylalpha-1,3 mannosyltransferase activity.
 7. The method of claim 1,wherein the enzyme is diminished or depleted by mutation of a host cellgene encoding the enzymatic activity.
 8. The method of claim 7, whereinthe mutation is a partial or total deletion of a host cell gene encodingthe enzymatic activity.
 9. The method of claim 1, wherein the attached Nglycans have seven or fewer mannose residues.
 10. The method of claim 1,wherein the glycoprotein comprises one or more sugars selected from thegroup consisting of galactose, GlcNAc, sialic acid, and fucose.
 11. Themethod of claim 1, wherein the glycoprotein comprises at least oneoligosaccharide branch comprising the structure NeuNAc-Gal-GlcNAc-Man.12. A method for producing a human-like glycoprotein in a Pichiapastoris host cell that lacks OCH1 activity comprising the steps ofdiminishing or depleting from the host cell an alg gene activityselected from the group consisting of: (a) an enzyme havingdolichyl-P-Man:Man₅GlcNAc₂-PP-dolichyl alpha-1,3 mannosyltransferaseactivity, (b) an enzyme having dolichyl-P-Man:Man₆GlcNAc₂-PP-dolichylalpha-1,2 mannosyltransferase activity, and (c) an enzyme havingdolichyl-P-Man:Man₇GlcNAc₂-PP-dolichyl alpha-1,6 mannosyltransferaseactivity; and introducing into the host cell at least one glycosidaseactivity.
 13. A method for producing a recombinant glycoprotein in aPichia pastoris host cell, the method comprising: (a) providing a Pichiapastoris host cell that lacks OCH1 activity and that has diminished ordepleted activity of one or more enzymes selected from the groupconsisting of: (a) an enzyme havingdolichyl-P-Man:Man₅GlcNAc₂-PP-dolichyl alpha-1,3 mannosyltransferaseactivity, (b) an enzyme having dolichyl-P-Man:Man₆GlcNAc₂-PP-dolichylalpha-1,2 mannosyltransferase activity, and (c) an enzyme havingdolichyl-P-Man:Man₇GlcNAc₂-PP-dolichyl alpha-1,6 mannosyltransferaseactivity, said host cell further expressing: (i) an α1,2-mannosidasecatalytic domain fused to a targeting peptide that targets theendoplasmic reticulum (ER) or Golgi apparatus in the host cell, (ii) aGlcNAc transferase I (GnT I) catalytic domain fused to a targetingpeptide that targets the ER or Golgi apparatus of the host cell, and(iii) a recombinant glycoprotein; and (b) growing the host cell underconditions to produce the recombinant glycoprotein, wherein therecombinant glycoprotein has N-glycans attached thereto comprisingGlcNAcMan_(x)GlcNAc₂ core structures, wherein X is 3 or
 4. 14. Themethod of claim 13, wherein the host cell further includes a nucleicacid molecule encoding a mannosidase II catalytic domain fused to atargeting peptide that targets the ER or Golgi apparatus of the hostcell and wherein the recombinant glycoprotein that is produced hasN-glycans attached thereto comprising GlcNAcMan₃GlcNAc₂ core structures.15. The method of claim 14, wherein the host cell further includes anucleic acid molecule encoding a GnT II catalytic domain fused to atargeting peptide that targets the ER or Golgi apparatus of the hostcell and wherein the recombinant glycoprotein that is produced hasN-glycans attached thereto comprising a GlcNAc₂Man₃GlcNAc₂ structure.16. The method of claim 13, wherein the host cell further includes anucleic acid molecule encoding a GnT II catalytic domain fused to atargeting peptide that targets the ER or Golgi apparatus of the hostcell and wherein the recombinant glycoprotein that is produced hasN-glycans attached thereto comprising a GlcNAc₂Man₃GlcNAc₂ structure.17. The method of claim 13, wherein the host cell further includes oneor more nucleic acid molecules encoding one or more sugar transportersselected from UDP-GlcNAc transporter, UDP-galactose transporter,GDP-fucose transporter, and CMP-sialic acid transporter.
 18. The methodof claim 13, wherein the host cell further includes one or more nucleicacid molecules encoding at least one enzyme activity selected fromgalactosyltransferase, sialyltransferase, fucosyltransferase, and GlcNActransferase III, IV, V, and VI.
 19. The method of claim 13, wherein thediminished or depleted enzyme has dolichyl-P-Man:Man₅GlcNAc₂-PP-dolichylalpha-1,3 mannosyltransferase activity.
 20. The method of claim 13,wherein the diminished or depleted enzyme activity is by mutation of ahost cell gene encoding the enzymatic activity.
 21. The method of claim20, wherein the mutation is a partial or total deletion of a host cellgene encoding the enzymatic activity.
 22. The method of claim 13,wherein the glycoprotein comprises one or more sugars selected from thegroup consisting of galactose, GlcNAc, sialic acid, and fucose.
 23. Themethod of claim 13, wherein the glycoprotein comprises at least oneoligosaccharide branch comprising the structure NeuNAc-Gal-GlcNAc-Man.24. A method for producing a recombinant glycoprotein in a Pichiapastoris host cell, the method comprising (a) providing a Pichiapastoris host cell in which OCH1 activity anddolichyl-P-Man:Man₅GlcNAc₂-PP-dolichyl alpha-1,3 mannosyltransferaseactivity of the host cell have been diminished or depleted, and whichcomprises one or more nucleic acid molecules encoding (i) anα1,2-mannosidase catalytic domain fused to a targeting peptide thattargets the endoplasmic reticulum (ER) or Golgi apparatus in the hostcell, (ii) a GlcNAc transferase I (GnT I) catalytic domain fused to atargeting peptide that targets the ER or Golgi apparatus of the hostcell, and (iii) a recombinant glycoprotein; and (b) growing the hostcell under conditions to produce the recombinant glycoprotein, whereinthe recombinant glycoprotein has N-glycans attached thereto comprisingGlcNAcMan₃GlcNAc₂ core structures.
 25. The method of claim 24, whereinthe host cell further includes a nucleic acid molecule encoding a GnT IIcatalytic domain fused to a targeting peptide that targets the ER orGolgi apparatus of the host cell and wherein the recombinantglycoprotein that is produced has N-glycans attached thereto comprisinga GlcNAc₂Man₃GlcNAc₂ structure.
 26. The method of claim 24, wherein thehost cell further includes one or more nucleic acid molecules encodingone or more sugar transporters selected from UDP-GlcNac transporter,UDP-galactose transporter, GDP-fucose transporter, and CMP-sialic acidtransporter.
 27. The method of claim 24, wherein the host cell furtherincludes one or more nucleic acid molecules encoding at least one enzymeactivity selected from galactosyltransferase, sialyltransferase,fucosyltransferase, and GlcNAc transferase III, IV, V, andr VI.
 28. Themethod of claim 24, wherein the diminished or depleted enzyme activityis by mutation of a host cell gene encoding the enzymatic activity. 29.The method of claim 8, wherein the mutation is a partial or totaldeletion of a host cell gene encoding the enzymatic activity.
 30. Themethod of claim 24, wherein the glycoprotein comprises one or moresugars selected from the group consisting of galactose, GlcNAc, sialicacid, and fucose.
 31. The method of claim 24, wherein the glycoproteincomprises at least one oligosaccharide branch comprising the structureNeuNAc-Gal-GlcNAc-Man.